As the two Incan leaders had been preoccupied with fighting each other, they missed the opportunity to attack the Spanish while their numbers were limited.
Many Spanish adventurers were still looking for their piece of land and the riches that came with it. Pizarro himself had already tried to infiltrate the Incan empire twice before.
For one thing the deaths of Aztec and Incan rulers touched off wars which made it easier to spread disease, because you know, the number one way to catch smallpox is via hand-to-hand combat.
During the reign of the emperor Huayna Capac, who lived ruled from 1492-1527, the Incas reached the height of their power. However, in less than ten years, the Incan empire would be no more.