Nick Hundley's sacrifice fly scored Miguel Tejada in the top of the ninth for San Diego, which moved 1 1/2 games ahead of San Francisco in the division. The Giants lost, 1-0, at home to the Los Angeles Dodgers Tuesday night.
Hundley's RBI turned out to be the game-winner as the Rockies scored twice in the bottom half off Heath Bell, but Colorado lost its second in a row following a 10-game skid and are now 3 1/2 games behind the Padres.
Todd Helton and Melvin Mora doubled to start the bottom of the ninth to produce one run. With one out, pinch-hitter Jay Payton singled to left-center to get Colorado within one. Pinch-hitter Jason Giambi, who hit the winning homer in the ninth inning against Arizona on Sunday, then walked. Eric Young Jr., though, grounded a ball to shortstop Tejada, who stepped on second before throwing to first for the game-ending double play.
Bell secured his 42nd save of the season, including his 29th in a row.
Jon Garland (14-11) snapped a three-start skid by allowing four hits and three runs -- one earned -- over seven innings. He had six strikeouts.
Jason Hammel (10-8) was charged with 10 hits and four runs over four frames to suffer the loss.
The Padres took the opener of the three-game set, 6-4 on Monday. This means Colorado has now suffered its first home series loss since July 27-29 vs. Pittsburgh. That's the only home series Colorado has lost since the All-Star break.
Tejada and Ryan Ludwick singled in runs in the top of the first, and the Padres padded their lead to 4-0 in the top of the fourth via David Eckstein's two-run double.
San Diego committed a pair of errors in the fourth, leading to Carlos Gonzalez's two-run double. He scored on Helton's sacrifice fly.
After wasting a chance with two men on base in the seventh, the Padres expanded their lead in the eighth. Will Venable singled with one out, and Stairs, hitting for Garland, belted a homer off Rafael Betancourt to center for the 6-3 cushion.
Gonzalez singled to center to drive in Ryan Spilborghs in the eighth.
The Padres, winners in six of their last nine games, clinched their first winning season since 2007...Bell's 42 saves ties a career-best, which he set last year...Colorado has already won the season series, which is now 11-6...Hammel fell to 3-1 lifetime against the Padres...Stairs expanded his major league record for pinch-hit homers, now with 22.