Colorado turned to Affeldt with two outs in the fifth inning after emergency starter Elmer Dessens had thrown 74 pitches -- his most in a game since 2005 -- in his Rockies debut.
Dessens' last pitch was a three-run homer to Mike Cameron that cut the Rockies' lead to a still manageable 6-5. But Affeldt (4-3), who had thrown 7 1/3 scoreless innings over his last 10 appearances, didn't retire a batter and gave up five runs on five hits.
The Padres scored nine runs in the inning, all with two outs. Gone was the Rockies' chance to win a road series, keep pace with the National League West-leading Diamondbacks and gain on the Wild Card-leading Padres. Colorado fell to six games behind Arizona and three back of San Diego.
The road trip continues with three games against the Dodgers.
Affeldt, whose hits against included a Terrmel Sledge two-run double and a Pete Laforest two-run homer, realizes he'll have to forget about the pain of the biggest inning against the Rockies since the Padres scored 12 in the ninth on Sept. 12, 2004.
"When your offense gives you nine runs, you're supposed to win those games," said Affeldt, who said he couldn't get his curve across for strikes. "But I didn't get an out. This is one of those games where you basically have to say what happens, happens.
"Obviously I've got to fix something. I'll fix it and pound the strike zone. And things will go our way."
The Rockies have overcome potentially devastating losses before during this season. A 1-9 road trip with four blown saves from then-closer Brian Fuentes didn't send them into the tank. But Thursday will stand as a blown opportunity to show they could win under trying circumstances.
"I have a lot of confidence in our personnel," Rockies manager Clint Hurdle said. "The nine-run inning was absolutely the furthest thing from my mind."
After Dessens, 36, was released by the Brewers at the start of August, the Rockies signed him to a Minor League contract. After one game with Triple-A Colorado Springs, the Rockies called him up because scheduled Thursday starter Aaron Cook (strained right oblique) became Colorado's third starter to go on the disabled list.
It had all the makings of a feel-good story. Dessens gave up two runs and three hits in the third, but he stopped the damage. A four-run top of the fifth, which included Brad Hawpe's two-run double, staked him to a 6-2 lead.
The story changed after Dessens had two outs and a man on first in the fifth. Geoff Blum popped a soft single. Then Cameron launched a fastball over the center-field wall. It was the first hit off Dessens by a right-handed batter in the game.
"If I make a better pitch to Cameron, I would have the lead," Dessens said. "I wish we would have gotten the third out in the fifth inning."
Affeldt's struggles, in part, are because he is struggling with left-handed batters, such as Sledge and Laforest. Lefties are batting .292 off him through 57 appearances. That's not good, since Affeldt is one of two left-handers in the bullpen. Fuentes is the other.
Matt Herges gave up the last of the nine runs to leave the deficit at 11-6. Troy Tulowitzki, Matt Holliday (two RBIs) and Garrett Atkins (two RBIs) had run-scoring singles in the sixth.
Nonetheless, Padres starter Clay Henley (2-3) won despite giving up six runs in five innings. Trevor Hoffman earned his 30th save of the season and extended his all-time record career total to 512.
Thomas Harding is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.