Buffalo Bill was the one she was after. The plot surrounded him.
The definition of an antagonist is a character who opposes the protagonist. The only thing Lector did was withhold infromation from Clarice until he was ready to talk about it. He never directly opposed her. Hell, he helped her. I suppose if anything that makes him more of an antihero. He was a bad guy, but he wasn't "the bad guy" of the movie. That was never the point of his character. His role was to supply the psychological tension and he did that wonderfully. He set the mood of the movie and that's why he's memorable.
But no, he wasn't the antagonist by a long shot, so I really don't think Silence of the Lambs counts as a movie where the bad guy wins.