Despite jumping out to a 3-1 lead in the fourth inning thanks in part to a two-run triple by Garrett Atkins, Colorado dropped its second game in a row and lost the series to the Padres, who won consecutive series from the Dodgers and Giants last week.
Colorado remains three games behind the first-place Dodgers, who fell to the Giants on Sunday, cutting the Rockies' advantage in the National League Wild Card chase to 4 1/2 games over San Francisco, where they open a three-game series on Monday.
"I think where we're going is going to be the best thing in the world for us," manager Jim Tracy said. "To get into that environment, and to realize we're staring right at the people that obviously have a chance to track you down, you stare them right in the face and go get them."
In the prior two games, the Rockies managed late-inning comebacks that helped them split those two contests, but could not regain the lead in this one and struggled to mount rallies offensively, a trend that stood out to Tracy.
"I think, obviously, what we're searching for right now, and it's going to come, is a solid offensive game," Tracy said. "Once again today, it wasn't there."
Todd Helton and Troy Tulowitzki, the third and fourth hitters in Colorado's lineup on Sunday, created ample opportunities for the offense by each reaching base in all four of their plate appearances. But only in the fourth did either player cross the plate.
"It goes without saying that we're not swinging the bats very well, and yet, I'm saying that for a little while now, and we've won 10 of 13 games in September," Tracy said. "We put ourselves in a decent position, but we've got to protect the lead. We weren't able to shut them down."
A three-run sixth inning for the Padres proved to be the decisive frame as Jason Marquis -- sporting a dominant record against San Diego this season at 2-0 with a 0.56 ERA in two starts -- fell apart and exited the game after issuing a bases-loaded walk to Everth Cabrera that pushed the Padres' lead to 5-3.
"I got away from what I do best, and that's sinking the ball on both sides of the plate," Marquis said. "I think I used my cutter a little too much today. As the game went on, I lost a little feel for my sinker, because I was going to my cutter a little too often. I just didn't get an out when I needed to, and I'm a little disappointed that I couldn't keep the game in check."
Marquis (15-11) lasted 5 2/3 innings while surrendering five runs on eight hits. He struck out three and walked four batters, and lamented serving up a lead as his club tries to protect its postseason chances.
"They did a great job putting runs on the board for me, and I just wasn't able to hold it," Marquis said. "Obviously, I'm not feeling good about myself right now, and I'm upset. The team got a loss, but hopefully we can change our fortunes around when we go to San Francisco."
Tracy saw a decline in Marquis' ability to command his sinker, but still focused on his club's lack of runs as the culprit in the series loss.
"What I thought was [Marquis' command] started really good," Tracy said. "Then it started to go the other way as we got into the middle innings. He lost his command somewhat to his glove side. But, obviously, as I said, with what we've done offensively here as of late, you have very little room for error, as far as that's concerned."
The Rockies scored three in the fourth against San Diego starter Clayton Richard, but were otherwise blanked by Richard. Helton drew three walks in the game, but was stranded on base three times as well.
"It would be great to score a lot more runs, there's no doubt about it," Helton said. "I think we can, and I think we probably will. As long as we're winning games, it's irrelevant. We need to start winning some games quickly, but you can't worry about it."
Colorado lost a second consecutive game for the first time since Aug. 29-30 in San Francisco, when they were swept by the Giants in a three-game set.
Tim Powers is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.