Indians were enslaved in Peru, but that was because Peru and Chile, IIRC, were basically private ventures, and were notable for their cruelty. Shortly after Columbus' discover, the colonization funded by the Spanish crown (such as the Caribbean and Mexico) was not permitted to enslave the Indians. There were even some priests in Mexico who were punished by the Inquisition for having enslaved Indians.
http://www.historyworld.net/wrldhis/PlainTextHistories.asp?groupid=1737&HistoryID=ab49
"It is calculated that as many as 200,000 Cubans and Spaniards die during the ten years of the war. Eventually, in 1878, peace is restored when the Spanish government promises extensive reforms including the abolition of slavery. This is granted in stages during the 1880s, but other promises are broken."
http://encarta.msn.com/encyclopedia_761595536_2/Spanish_Empire.html
"The Spanish colonists tended to settle where the native population was most plentiful. These tended to be urban areas and many were sites where the Spanish had built their own city on an existing native city or town. Cortés provided a model for this when he built Mexico City over the conquered Aztec capital of Tenochtitlán. He introduced to Mexico many crops and industries familiar to Spaniards, such as sugar, silk, cattle, wheat, and cotton, and he instituted gold and silver mining and the slave trade."