The boarding passes in Brazil have stickers with a barcode, wich are read by the guards when you enter the security area, and those barcodes actually indicate you have paid the taxes. As you will be in transit, your passes will not have these stickers, and I suppose you will have to pay them, otherwise you will not be allowed to board.
(This is an educated guess, haven't done what you describe here)
If you check in for the next leg at GRU you will get passes with barcodes, that will mean you will not have to pay anything extra.