After the arrival of appointed royal viceroy Blasco Núñez Vela in 1544, Gonzalo succeeded to have him repelled and sent to Panama in chains.
The two met on January 18 at Iñaquito in the outskirts of Quito, present-day capital of Ecuador, where the superiority of the Nueva Castilla army ensured victory for Gonzalo.
Blasco Núñez Vela reportedly fought but fell as a victim in battle and was later decapitated on the field of defeat, a fate Gonzalo himself would share two years later at Jaquijahuana.
The said viceroy arrived with the strong intention of enforcing the recently enacted New Laws that abolished the encomienda prohibited the personal labor of the indigenous people.
The encomenderos (the masters) protested and organized a rebellion, choosing Gonzalo Pizarro as leader, who was then a wealthy encomendero in Charcas (present-day Bolivia) Gonzalo went to Cuzco, where he was magnificently received and proclaimed Attorney General of Peru to protest the New Laws before the Viceroy and, if necessary, before the Emperor Charles V himself (1544).
In Lima, the viceroy Núñez Vela was hated for his capriciousness, even to the extreme of killing a prominent resident of the city, an administrator by the name of Illán Suárez de Carbajal, with his own hands.
The judges of the Royal Audience, in their eagerness to gain popularity, were inclined to defend the rights of the encomenderos and take the Viceroy prisoner.
It was then that Pizarro planned an intelligent strategy to draw the viceroy out of Popayán, a position that he was finding difficult to attack: leaving a small garrison in Quito, under the command of Pedro de Puelles, Pizarro appeared to march south with his entire army, instructing their indigenous allies to spread the story that he was marching to aid Carvajal against Centeno.
Since it was too late to head back, so the viceroy withheld this news from his troops, so as not to discourage them, and continued to advance, already deciding to go to battle.
The superior of the Franciscans, who was also pessimistic, offered refuge for Blasco Núñez in his convent and invited Benalcázar to retire as soon as possible, propositions which were ignored.
The viceroy, considering the difficulties of mounting a defense in the city, rallied his troops and gave orders to leave and do battle outside of Quito.
Pizarro gave a fiery speech, whose final phrases were: "Gentlemen, to fight a defend your freedom, life and property."
The viceroy, who valiantly fought in the left flank, was finally reached by a blow from Hernando de Torres (a resident of Arequipa), receiving a mortal wound in the head.
However, a little while later he was recognized by a soldier and the news reached Benito Suárez de Carbajal, whose brother Illán had been murdered in Lima by the viceroy.
They were followed for a while by Pizarro's riders, until night fell and Gonzalo sounded the trumpets, gathering his troops and putting an end to the battle.
Thanks to influential residents, the body and the head were collected for a decent burial in the cathedral of Quito, later to be transferred to the viceroy's land, Ávila, in Spain.