The Spaniards didn't go deep into the Amazon. It was possible to hide from them in the jungle, which is thousands of miles deep.
The whole Amazon civilisation was not wiped out.
It took a giant hit in the early 20th century when the automobile industry required rubber for tires, which it got by enslaving and brutally murdering indigenous Amazonians.
Then later in the 20th century vast tracts of the Amazon were converted into coffee farms. The habitat loss decimated indigenous Amazonians, but it hasn't wiped them out.