From what I understand, it appears that the Amazonian basin was much more inhabited than previously tought, with farming populations and relatively complex social structures.
Which kind of societies are we talking about there? Did they had relations with Andine cultures (and if it's the case, did these relations played a major role as a primary/secondary cultural dynamic?)
What caused their collapse? The epidemic shock alone or colonial progression?
Which secondary or tertiary sources would you recommand on the topic?
South America is not my area of expertise, so I will refrain from embarrassing myself by directly answering the question. However, I can point you to some secondary reading on this topic.
The book most relevant to your question would be Jerry D. Moore's A Prehistory of South America: Ancient Cultural Diversity on the Least Known Continent, 2014, which you can find on JSTOR. It looks in detail at both agricultural and social developments in pre-colonial South America, and also gives good historiographical overviews both in text and notes. Refreshingly for an academic book, it has plenty of relevant pictures (!). It is aimed at undergraduates, and should provide a good introduction to scholarly debate.
You can also pick up The Cambridge History of the Native Peoples of the Americas, Vol. III: South America, Part 1, ed. by F. Salomon and S. Schwartz, 1999, which has several chapters on Amazonian civilisations. You might find the chapter by Thomas Lynch, 'The Earliest South American Lifeways' relevant to discussions of 'civilisation' in the Americas.
For the collapse of native culture in the Amazon, read Monteiro's 'The Crises and Transformations of Invaded Societies: Coastal Brazil in the Sixteenth Century' in the Cambridge History mentioned above. John Hemming's Red Gold: The Conquest of the Brazilian Indians, 1978, and his newer Tree of Rivers: The Story of the Amazon, 2008, are also good introductions to the collapse by the well respected former director of the Royal Geographical Society.