The answer to this can be found in Chapter 3. There, Diamond explains how the Spanish were able to defeat the Inca. Beginning on page 77 in the paperback edition of the book, he discusses the role of disease. Basically, diseases killed important Inca men and caused a civil war to happen.
Although diseases (in particular, smallpox) killed many Incas, it was not mass mortality that weakened the Inca people. Instead, it was the fact that the Inca emperor had died of smallpox. In addition, the person who was designated to be his heir was killed by the disease. This meant that there was no one who was acknowledged by all to be the leader. In that situation, a civil war erupted. Atahuallpa fought with his half brother Huascar for power. Because of the civil war, which ended right before the Spanish got to Cajamarca, the Inca were not particularly strong or united when the Spanish arrived.
Thus, disease helped the Spanish conquer the Inca by killing important Incas and causing disunity in the empire.