Nick Hundley and Jedd Gyorko added solo home runs to the 12-hit San Diego attack, and Alexi Amarista chipped in two hits and an RBI.
Jeff Manship (0-2) took the loss in his second start of the season. Manship gave up six runs on eight hits in five innings. The loss ended Colorado's four-game winning streak.
Wilin Rosario and Charlie Culberson had two RBI apiece for the Rockies.
Colorado also compiled a dozen hits Tuesday and got off to a fast start that gave them a 4-1 lead after the first inning. San Diego came back with four in the top of the second and led 6-4 in the fifth inning when Colorado scored their final run.