I would say that his first conscious act of rebellion is when he tells the Giver that he thinks that Sameness was a bad thing. This happens right at the end of Chapter 12.
Up until that point, Jonas has pretty much just been doing as he is told. He has not been trying to think too much for himself or question the basis of his society.
But, in the part I am referring to, Jonas finds out that Sameness is the reason that people can no longer see colors or sunshine. He thinks that these are too great of sacrifices and he tells the Giver "We shouldn't have!"