None of the 4 categories that San Andreas was nominated for at the Game Developers Choice Awards won Rockstar an award. GTA San Andreas was nominated for best game, audio, game design and writing.
The GDC awards are unique in the industry because game developers get the opportunity to award each others' work, instead of consumers voting for their favourite. Big winner of the night was Half-Life 2 with 4 awards.
Related link: GDC Award Winners