What happened was tuberculosis, influenza and measles.
These diseases, inadvertently introduced into the Americas by the newly arrived Europeans, spread like wildfire through the indigenous populations.
Literally millions died, 99% of whom never met a European or even knew of their existence. There is little doubt that this is what happened in the Amazon.
There have been a number of past posts on this subject here on FR. After I do a bit of research, I'll post the links if I can find them.