He needed Atahualpa alive, as he was the source to the gold Pizarro and his men were after.
With Atahualpa's capitulation, Pizarro gained control of a vast portion of Tawantinsuyo, from Tempula river (Colombia) to the north, reaching down to Cuzco, including Machu Picchu, the fortress city they've fortunately never discovered.
Machu Picchu remained unknown to the world for some four hundred years.
The secret city of the Incas was discovered by Yale Professor Hiram Bingham in 1911.
To learn more about this, refer to Machu Picchu and Inka Trail pages.
Just outside Cuzco, in the fortress of Sacsayhuaman, the final battle against the Incas took place, and Spaniards finally gained control of Tawantinsuyo.