Hoffman allowed three consecutive extra-base hits in the bottom of the 13th inning and a sacrifice fly to Jamey Carroll as the Rockies rallied for a 9-8 victory before a sold-out crowd of 48,404.
The Rockies advance to face the Phillies on Wednesday in the National League Division Series in Philadelphia while the Padres (89-74) -- who held the Wild Card lead from Aug. 2 up until Monday -- were left to ponder what could have been.
But what they won't ponder is who should have been standing on the mound in the 13th inning, trying to close out a victory that certainly seemed within reach, especially after Scott Hairston's two-run home run in the top of the inning.
"We don't want anyone but [No.] 51 taking the ball," said Padres outfielder Brian Giles, whose throw home in the 13th inning on Carroll's fly ball reached the plate before Holliday, although the ball was jarred loose on the play.
Carroll's fly ball touched off a raucous celebration while many of the Padres stood on the top step of the visiting dugout watching the party and likely lamenting how close it was to being them celebrating and heading to Philadelphia.
"Guys in this room should be proud," Giles said, surveying the clubhouse. "They grinded all year and put ourselves in a position for the postseason. We have nothing to be ashamed about."
Hoffman, as he does after save or blown save alike, held court in front of his locker and took full responsibility for the loss just as he did Saturday in Milwaukee, after allowing a game-tying RBI triple to Tony Gwynn Jr. in an extra-innings loss that also kept San Diego from clinching a playoff berth.
In 31 career appearances at Coors Field, Hoffman is 1-4 with a 6.03 ERA and 20 saves.
"We can't point to any other factor but my performance tonight," said Hoffman, who finished the season with seven blown saves. "It's a burden I have to deal with. I strive for consistency. To barely get an out tonight is pretty devastating."
Carroll's fly ball ended what was a wild affair between the Rockies (90-73) and Padres, a game that saw the Padres use 16 different position players and five different pitchers. The Rockies used 13 position players and 10 pitchers.
San Diego pitcher Jake Peavy, gunning for his 20th victory of the season, struggled nearly from the start, allowing two runs in the first inning. He gave his team 118 pitches, but left after 6 1/3 innings having allowed six runs on 10 hits.
"Just a tough night," Peavy said, shaking his head.
It was on a lot of fronts for the Padres hitters, who were 3-for-16 with runners in scoring position and stranded 13 baserunners. San Diego finished with 15 hits, including two big blows that accounted for seven of its runs.
Trailing, 3-0, San Diego took a 5-3 lead when Adrian Gonzalez hit his 30th home run of the season, a grand slam off Rockies starter Josh Fogg. But there wasn't much offense for the Padres until Hairston's two-run shot to left-center field off Jorge Julio.
Center fielder Brady Clark, filling in for an injured Mike Cameron, had a tough time on defense. Clark missed a fly ball when he dove for Troy Tulowitzki's double in the fifth inning. Tulowitzki would eventually score.
In the sixth inning, Clark couldn't run down Seth Smith's triple to the wall in center field, which was struck well, or Tulowitzki's triple later in the inning. He also threw wide of home on Kaz Matsui's sacrifice fly.
There were positives for the Padres, as after Peavy left, the bullpen that was overworked in Milwaukee combined for 5 2/3 scoreless innings, with an impressive and season-high 2 2/3 scoreless innings from Heath Bell, who finished with five strikeouts. Doug Brocail and Joe Thatcher also pitched well.
"It was a great game, a game people around the country were probably enthralled with from the first inning on," Padres manager Bud Black said. "I made a couple of comments to the coaches what a great game it was."
It just didn't end the way the Padres would have liked, not the game and not the season.
"If it wasn't for those two guys [Peavy and Hoffman], we wouldn't be in that position," Black said. "It's a rare occurrence [a Hoffman blown save] ... but the Rockies came out swinging. But I'll take my chances with Trevor."