While these vacillatory measures were going on at the viceregal palace, information was brought to the oydors, that the viceroy had drawn out his troops in the great square, with the intention of attacking them. Having as yet collected only a small force for their protection, they resolved to go out into the street; believing, if the viceroy should come to blockade them, and should occupy the streets leading to the house of Cepeda, that all those who were disposed to aid them would be intercepted. They advanced therefore by the streets which led towards the great square, and were soon joined by others of their adherents, to the number of about two hundred men. To justify their conduct on this occasion, they caused the act which they had drawn up to be publickly read; but so great was the noise and confusion, that very few of those present were able to hear its tenor. On the arrival of the judges and their partizans in the great square, day began to dawn. At this time, the troops attached to the viceroy fired a few musket-shots, from the corridore of the palace, and began to extend themselves in front of the main gate. The soldiers who accompanied the oydors were much displeased at this procedure, and proposed to assault the palace, and to slay all that resisted them; but the oydors restrained and appeased them. The oydors then deputed Gaspard de Carvajal, the superior of the Dominicans, and Antonio de Robles, to inform the viceroy, that their only demand from him was an assurance that they should not be compelled to embark against their will and contrary to the express orders of his majesty, which fixed their residence at Lima. They farther required, that, without proceeding to hostilities, the viceroy should come to the great church, where they proposed, going to meet him, and where all their differences might be amicably settled; as otherwise he would put both himself and all who were with him in extreme danger. While these envoys were in the palace in the execution of their commission, the hundred soldiers who formed the guard of the viceroy went over in a body to the oydors; by which, as the entrance to the palace was left entirely unguarded, several of the malecontents got admission to the chambers belonging to the officers of the viceroy in the outer court, which they pillaged. At this time, the licentiate Ortiz de Zarate went from his house towards the palace, meaning to have joined the viceroy; but meeting the other oydors on his way, and seeing that it was impossible for him to prosecute his original design, he accompanied them to the church.

When the viceroy received the message of the oydors from Carvajal and Antonio de Robles, considering at the same time that his palace was already in possession of the insurgents, and that his own troops had abandoned him, he determined to proceed to the church, and to give himself up to the oydors who there waited for him. They carried him directly, in his coat of mail and cuirass, to the house of Cepeda; where, seeing Ortiz along with the other judges, he exclaimed: "Is it possible that you, in whom I had so much confidence as one of my best friends, have joined with the rest in making me a prisoner." To this the licentiate replied, "Whoever has told you so spoke falsely, as it is known to every one who those are that have caused you to be arrested, and that I have no share in the matter." The three other judges gave immediate orders to convey the viceroy on board ship, that he might be sent to Spain; justly fearing, if Gonzalo Pizarro should find him in custody on his arrival at Limn, that he would put him to death, or that the relations and friends of the commissary Suarez might kill him in revenge for the murder of that officer; as in either of which cases the blame might be imputed to them, the judges were much embarrassed how best to act in this delicate emergency, considering that if they merely sent the viceroy on board the fleet which lay at anchor off the harbour of Calao, he might be soon in condition to return in force against them. In this dilemma, they appointed Cepeda, one of their number, to act as captain-general of the colony; who, with a strong guard, conducted the deposed viceroy to the sea side on purpose to put him on board one of the ships. They found some difficulty in executing this measure, as Diego Alvarez de Cueto, who commanded the fleet, on seeing the assemblage of people on the shore, and learning that they had the viceroy among them as a prisoner, sent Jerom de Zurbano, one of his captains in an armed boat to collect all the boats of the fleet, with which, accompaniment he approached the shore and demanded the liberation of the viceroy from the judges. This measure was altogether ineffectual, as the judges refused to listen to the demands of Cueto; who, after exchanging a few shots with those on shore, went back to his ships.

After this, the judges sent off a message to Cueto, by means of Friar Gaspard de Carvajal, in which the deposed viceroy concurred, ordering him to surrender the command of the fleet, and to give up the children of the late marquis, in return for which they would place the viceroy under his charge, who would otherwise be in great peril of his life. On getting aboard ship, Friar Gaspard presented his commission to Cueto and gave him a full account of the state of affairs, in presence of the licentiate Vaca de Castro, who still remained a prisoner in that vessel. In consideration of the danger to which the viceroy was exposed, Cueto sent the children of the marquis on shore together with Don Antonio de Ribera and his wife who had the care of them. The judges still insisted that Cueto should surrender the fleet to their command, threatening to behead the viceroy if he refused; and though Vela Nunnez, brother to the viceroy, went several times with messages to induce compliance, the captains of the ships would not consent to that measure, so that the judges were constrained to return to Lima with the viceroy still in custody.

Two days afterwards, the commanders of the ships were informed that the judges and their partizans had come to the resolution of sending a strong force of musqueteers in boats to make themselves masters of the ships by force. They might perhaps have easily persuaded Cueto to give up the fleet, of which in reality Jerom de Zurbano had more the command than he, as all the soldiers and sailors who were attached to the deposed viceroy were at his disposal; but Zurbano, to whom the judges made great offers, was quite inflexible. The captains of the fleet came even to the resolution of quitting the port of Lima, to cruise upon the coast of Peru, till such time as they might receive orders from his majesty how to conduct themselves in the present crisis. They believed that the viceroy had many friends and adherents in Lima and other parts of Peru; as many persons who had not taken any share in the deposition and imprisonment of the viceroy, and several of those who were best disposed to the royal service continued almost daily to make their escape on board the fleet. The ships were tolerably well armed and appointed, having ten or twelve iron cannon, and three or four of brass, besides forty quintals of powder. As to provisions, they had above four hundred quintals of biscuit, five hundred bags of maize, and a large store of salt meat; so that they were victualled sufficiently for a considerable time, and they could easily procure water on any part of the coast. Their force however was very small, as they had only twenty five soldiers, and by no means a sufficient number of mariners for the ten ships which composed their fleet. They resolved therefore to abandon four of the smallest vessels, which they were unable to man; and not thinking it right to leave these behind, lest they might have been employed against themselves by the partizans of the judges, they set these small vessels on fire the day after the imprisonment of the viceroy, as likewise two fishing barks which were in the harbour, and then set sail. The four small ships were entirely destroyed, but the two fishing vessels were saved after sustaining very little damage.