Pomeranz (1-4) also struck out five Phillies, but that's small consolation as the Rockies fell to 3-12 on Sundays, squandering a chance at winning their first outright series since early June.
The Rockies nicked Phillies lefty Cole Hamels (11-4) for one run in eight innings, thanks to a Carlos Gonzalez RBI triple in the sixth inning, but couldn't add more. With Gonzalez at third and one out, cleanup hitter Ramon Hernandez struck out and Michael Cuddyer grounded out to end the frame.
Hamels gave up leadoff singles to the Rockies in the first three innings, and still got out of each of them without a threat.
"When you're dealing with a guy like Cole Hamels, when situations present themselves, you have to seize them," Rockies manager Jim Tracy said. "Unfortunately we didn't do that."
With runners on first and second and none out in the first, Gonzalez and Hernandez each whiffed at Hamels changeups and Cuddyer grounded out.
"It's just trying to make one pitch," Hamels said. "When you get guys on, you don't want them to score. You're just trying to take one pitch at a time and try to make the best pitch you possibly can and hope you get the groundouts or the strikeouts."
Hamels struck out two more in the second after Tyler Colvin singled to left to get things started. Fowler, who was the only player to get more than one hit off Hamels, began the third with a single, but was picked off.
"He's a good pitcher, you've gotta get whatever you're going to get quickly," Fowler said, noting that Hamels gets better as the game goes on. "He pitches you differently every time."
Since July 5, Fowler is batting .464 (13-for-28) with six multi-hit games.
As Pomeranz's pitch count began to climb, it looked like he'd be saddled with another tough-luck loss. Before winning July 6 at Washington, Pomeranz lost despite giving up one unearned run in six innings to the Padres on July 1 in his first start since early May.
The fifth inning appeared to be going fine, after strikeouts of Mike Fontenot and Hamels. But Jimmy Rollins slapped a single through the left side of the infield and Shane Victorino drew a four-pitch walk.
"Never good when you have a two-out walk," Pomeranz said.
Pence then snapped his 0-for-13 slump with his 17th homer of the season.
"That's what Hunter Pence does when you hang breaking balls down the middle of the plate," Tracy said. "He hits them out of the park."
Tracy praised Hamels after the game, listing his six-hit outing among the best performances by an opposing pitcher he had seen this season, rivaling Barry Zito and C.J. Wilson. It was just the fifth time this year the Rockies have been held to one run or less at home.
"It's tough, you get to the heart of the order, and you have to make your pitches," Hamels said. "And then to keep the long ball away. It's the type of park where you make one mistake and leave the ball up, it's going to be out of here."
That's something Pomeranz was reminded of, in painful fashion.
"I made a few bad pitches today," Pomeranz said. "And they made me pay for it."