It’s important to remember that Natives began to die from European diseases, such as mumps, measles, smallpox, and influenza, shortly after contact. Natives carried zero resistance to these diseases that began to spread more quickly than the European explorers and some of the densely populated regions of Central and South America would lose up to 90% of their local population. (The Inca Empire had a vast network of roads, bridges, and runners that allowed messages to travel up to 150 miles a day. Systems like this would allow disease to spread just as quickly).

Despite a sick and weakened population, Natives were some of the first people Europeans tried to enslave to work the crops and mines of the New World. However, Natives knew the land and had connections to family and friends so they were much more prone to runaway than an African slave. By enslaving Africans, Europeans were able to eliminate or minimize many of the issues that arose through Native enslavement.

EDIT: I'm sorry, it was 4am when I wrote this and I feel I should clarify a bit.

Natives were absolutely still enslaved throughout the Americas and it didn't stop with the arrival of African slaves. Spaniards would implement the encomienda system where they argued they protected the Natives from outsiders in exchange for labor. In reality, they were taking them from their homes, repressing their language and customs, and forcing them to work in miserable conditions. The silver mines in Peru and Potosí (now Bolivia) are a good example of this. Natives were also exposed to dangerous amounts of mercury in addition to silver since they were forced to mine mercury to use in the extraction of silver from silver ore.

I had also forgot to mention that the Catholic Church worked on converting Natives to Christianity and teaching them European ways; these missions took people away from their own culture, but also protected some of them from plantation owners and enslavement.

Anyways, Europeans were unable to rely solely on Native labor and quickly turned to African slave labor to supplement the labor shortage.

Sources

Early Modern Europe, 1450–1789 by Merry Wiesner-Hanks

Natives and Newcomers: The Cultural Origins of North America by James Axtell

Native Americans were enslaved, often, from the earliest Spanish outposts in the Caribbean, to late into the 1800s/early 1900s throughout the New World. Slavery was part of the toxic colonial cocktail that decreased population size and prohibited demographic recovery, though much of this history is forgotten in popular culture. Check out these previous answers on captives taken back to Europe, or on the scale of Native American slavery in the Southeast for more information.

Also, Resendez recently published an amazing book on Native American slavery called The Other Slavery: The Uncovered Story of Indian Enslavement in America that I highly recommend if you would like to learn more about this topic.

Follow up, in Why Nations Fail the authors made the claim that, while the English and French colonists may have wanted to copy the Spanish model of enslaving/dominating natives, the combinations of factors of now-CONUS/Canada of low population density, less political centralization, lowered immunity and native's greater familiarity with the land due to a less urban/settled lifestyle, the English and French were forced have their labor force be comprised of themselves. The authors argue that this initial difference in social structure was the greatest single factor in what made US and Canada so much more prosperous than former Spanish colonies.

What do the more knowledgeable members think about that argument?

Follow up: In my highschool History lessons in Portugal, it was taught that Africans were preferred to Native American slaves for the simple reason that the former handled hard work better, while the latter were physically weaker and would die if subjected to the same conditions.

While to me now it seems like a somewhat racist view of the issue, I wonder why I was taught that. Is this idea contemporary to the Atlantic slave trade?

And if the reason Africans were prefered in America was to do with the lack of familiarity and contacts, why were they also prefered in Europe?