While the artillery on both sides kept up a constant fire, the royalist army descended from the mountain without keeping any regular order, and in all possible haste, the cavalry all on foot leading their horses, both on account of the ruggedness of the ground and the better to avoid the cannonade from the enemy, as they had no shelter from the balls. Immediately on getting down to the plain, the troops were drawn up in order of battle; the infantry in two battalions in the centre, and the cavalry on the two wings. The cavalry of the left wing was commanded by the captains Juan Saavedra, Diego de Mora, Rodrigo Salazar, and Francisco Hernandez de Aldana. The royal standard was displayed by the licentiate Carvajal in the right wing, in which likewise were posted the captains Don Pedro de Cabrera, Alfonso Mercadillo, and Gomez de Alvarado. The infantry marched between the wings of horse, but a little farther in advance, under the captains Ramirez, De Castro, De Solis, Cardenas, Menezes, Mosquera, De la Cerna, Urbina, Aliaga, De Robles, De Arias, and De Olmos. A little in advance of the infantry, Alfonso de Mendoza marched with his troop of horse to commence the attack, accompanied by Centeno, who was determined to exert himself on this occasion in revenge for his defeat at Guarina. Pedro de Villavicentio acted as serjeant-major or adjutant-general of the army. The president, accompanied by the archbishop of Lima, was a little on one side, on the slope of the mountain, by which the major-general Alvarado and Valdivia brought down the artillery and the three hundred musqueteers commanded by Mexia and Palomino. On getting into the plain, this body of musqueteers divided in two, Mexia marching to the right along the river, and Palomino keeping to the left along the skirts of the mountain.

While the royalist artillery was coming down the mountain, the licentiate Cepeda, Garcilasso de la Vega, and Alfonso de Piedra, with several other persons of rank and some private soldiers, abandoned Gonzalo to surrender themselves to the president. They were closely pursued by Pedro Martin de Cicilia and some others of the insurgents, who wounded several of these deserters. The horse of Cepeda was killed under him by the thrust of a lance, and himself wounded, and he had assuredly been either taken or killed unless promptly succoured by order of the president. In the mean time Gonzalo kept his troops in firm array, waiting for the enemy, and in expectation that they might attack him in confusion and be easily defeated, as had happened in the battle of Guarina. Hinojosa on his side, advanced with the royalists in the best order and at a slow pace, to within musquet-shot of the insurgents, where he halted in some low ground, in such a situation that his men were secure from the cannon-balls of the enemy, which all flew over their heads, although the gunners used every effort to depress their guns so as to fire low. At this time the platoons of musquetry on the wings of both armies kept up a close fire, Alvarado and Valdivia using every effort to cause their men take good aim, while the president and archbishop encouraged their gunners to fire quickly and to purpose; making them often change the direction of their guns, as circumstances appeared to require.

Observing that several of the soldiers of Gonzalo were endeavouring to abandon him and were hotly pursued, Centeno and Mendoza advanced with the cavalry under their command, on purpose to protect all who wished to come over. All those who quitted the insurgents, urged the commanders of the royal army not to advance to the charge, as they were certain the far greater part of the army of Gonzalo would abandon him, so that he would be easily defeated without any danger to the royalists, and with little effusion of blood. At this time, a platoon of thirty musqueteers, finding themselves near the royal army, came over in a body and surrendered themselves. Gonzalo wished to have these men pursued and brought back; but the attempt threw his troops into confusion, and his whole army began instantly to break up, some fleeing towards Cuzco, while others went over to the president and surrendered themselves. Some of the insurgent officers were so confounded by this sudden and universal derout, that they neither had presence of mind to flee or to fight. On seeing this hopeless turn of his affairs, Gonzalo lost all courage, and exclaimed in despair, "Since all surrender to the king, so must I also." It is reported, that Juan d'Acosta endeavoured to encourage him, saying, "let us rush upon the thickest of the enemy, and die like Romans;" to which Gonzalo is reported to have answered, "It is better to die like Christians."

At this time, Gonzalo observing the serjeant-major of the royalists near him, surrendered to him, giving up a long small sword which he had used instead of a lance, as he had previously broken his lance upon some of his own men who were running away. He was immediately conducted to the president, to whom he used some very imprudent expressions, and by whom he was committed to the custody of Centeno. About the same time with Gonzalo, most of his officers were made prisoners. The lieutenant-general Carvajal endeavoured to save himself by flight, meaning to hide himself among some tall reeds in a marsh during the night; but his horse stuck fast in the morass, and he was brought prisoner to the president by some of his own men. In the pursuit, some of the insurgents were killed, but most of their officers were made prisoners.

After the entire derout of the enemy, the soldiers of the royal army pillaged the camp of the insurgents, where they made a prodigious plunder in gold, silver, horses, mules, and rich baggage, by which many of them acquired considerable riches, some individuals having acquired so much as five or six thousand ducats. One of the soldiers happened to fall in with a fine mule having a load on his back, which seemed to consist only of clothes, he therefore cut the cords and threw off the load, carrying off the mule alone; immediately after which three other soldiers, more experienced in such matters, opened up the pack, which they found to contain a considerable quantity of gold and silver wrapped up in Indian cloaks for better concealment, worth five or six thousand ducats.

As the army was much fatigued by the operations of that day; besides being under arms all night, the president allowed the men to rest one day, yet thought it necessary to dispatch the two Captains Mexia and De Robles with their companies to Cuzco, to prevent those soldiers who had pursued the fugitives towards that place from entering and plundering the city and killing a number of the inhabitants; more especially as many might now feel inclined to act from particular enmity towards such as had given them offence during the late troubles, under pretence of following up the victory. Those captains were likewise directed to secure such of the officers and soldiers of the defeated army as had fled in that direction. Next day, the president gave orders to the licentiate Cianca, one of the new oydors, and Alfonzo de Alvarado, his major-general, to bring the prisoners to trial. No other proof was requisite against Gonzalo Pizarro than his own acknowledgment and the notoriety of his having been in open rebellion against the sovereign. He was condemned to be beheaded, and that his head should be fixed in a niche or recess on the gibbet at Lima, secured by a trellis or net-work of iron through which it might be visible, with this inscription above. "The head of Gonzalo Pizarro, a traitor and rebel, who revolted against the royal authority in Peru, and presumed to give battle to the army under the royal standard in the valley of Xaquixaguana." His whole estates and property of every kind were confiscated; and his house in Cuzco was ordered to be rased, and salt sown upon its scite, on which a pillar or monument was to be erected with a suitable inscription to perpetuate the remembrance of his crime and condign punishment. Gonzalo was executed on the day of his trial, dying like a good Christian.