Winners of eight straight, the Rockies moved to 1 1/2 games behind the Padres in the National League Wild Card race, with the Phillies in between the two, a half-game behind.
The Rockies have won the last two despite the absence of NL Most Valuable Player candidate Matt Holliday, who has a left oblique strain but hopes to return Tuesday.
The Rockies' 84th victory broke a club record, and left-hander Jeff Francis (17-8) pitched eight strong innings, yielding seven hits and two runs, to match Kevin Ritz (1996) and Pedro Astacio (1999) for the club victory mark.
The current win streak is one game shy of the club mark of nine (Aug. 25-Sept. 5, 1997). The Rockies will begin a three-game road set with the Dodgers on Tuesday night, and finish the regular season with three at home against the NL West-leading Diamondbacks starting Friday night.
Atkins' homer was a happy oddity, but the Rockies won with another solid all-around display led by Francis, who struck out eight.
Since enduring an eight-run, eight-hit beating in a road loss to the Phillies on Sept. 13, Francis has beaten the Dodgers and the Padres by posting a 1.84 ERA, with more strikeouts (18) than baserunners (17, on 13 hits and four walks).
"This is a club that has not been one of his better matchups, and this park particularly," Rockies manager Clint Hurdle said of Francis, who entered Sunday 4-10 with a 6.17 ERA in his career against the Padres, and 2-5 with a 6.14 ERA at PETCO.
"I felt like I had good fastball command going, and I think I had a few 1-2-3 innings in a row, and confidence grew," Francis said.
Meanwhile, the Rockies peppered Padres starter Greg Maddux (13-11) for eight hits and five runs in 3 2/3 innings. Todd Helton extended his hit streak to eight games with two hits and two RBIs, and Brad Hawpe went 2-for-3 with his 28th home run of the season to finish 8-for-15 with two homers for the series. Ryan Spilborghs added an RBI triple.
The Rockies began coming together last season, with a whole group of homegrown players establishing themselves as starters, but big-name pitchers such as Maddux routinely shut them down.
"I guess it used to affect us adversely, but we've faced him so much, and everybody knows that they belong," said Hawpe, whose ninth-inning homer off reliever Justin Hampson made him 5-for-his-last-5 against left-handed pitchers -- the bane of his batting average this season.
But Hawpe can smile about facing lefties, just like Atkins can laugh about his circuit of the bases. He couldn't recall an inside-the-park homer past his youth, when the lack of a fence made such plays possible.
Next time Helton calls him "Fankles," to tease him for having "fat ankles," Atkins can point to the record book.
"I've seen it all now," Helton said. Asked if he can match Atkins, he said, "There'd have to be a train wreck, just like there was for 'Atty's.'"
Atkins' inside-the-park job was the ninth in Rockies history, the first since Dustan Mohr did it July 10, 2005 against the Padres' Dennys Reyes at Coors Field, and the first at PETCO since current Rockies second baseman Kazuo Matsui's for the Mets on April 20, 2006.
"Everyone is saying I kind of move up the ranks on the speed chart for the team. ... I guess it's just me and 'Kaz' at the top," Atkins said. "Once I get to top speed, I'm pretty fast. It takes awhile to get there."