The disease that killed Huayna Capac and many other Inca was smallpox.
During the Conquest of America, smallpox was infected by the newcomers to the Native Americans, who were totally lacking in defense against this disease unknown to them, causing a demographic collapse in the native populations.
Among the Incas the smallpox ended with the monarch Huayna Capac, provoked the civil war prior to the Spanish appearance and caused a demographic disaster in the Tahuantinsuyo, which before the arrival of the Spaniards had 14 million inhabitants, while towards the 18th century had just 1.5 million.