Thomas broke a scoreless tie in the 41st minute, blasting a header from the penalty box off a corner kick from Powers.
Powers doubled the advantage with a goal of his own just 6 minutes later when Edson Buddle fed him a pretty through ball between two Galaxy defenders and the Colorado midfielder notched his fourth goal of the season.
The Rapids (9-7-7) came into the contest one point out of the fifth and final Western Conference playoff spot.
The Galaxy, meanwhile, fell to 10-9-3. They held the West's third position with 33 points starting Saturday's play.