Starter Tyler Cloyd, pitching on three days' rest, left after giving up a three-run homer with no outs in the fourth. With 18 outs to get, the Phillies' bullpen stood strong through the seventh inning.
In the eighth, though, Astros pinch-hitter Jed Lowrie doubled off reliever Jake Diekman, scoring two and giving the Astros a one-run lead. Brandon Barnes followed with an RBI single to give the Astros an insurance run.
The Phillies couldn't rally off closer Wilton Lopez in the top of the ninth.
Right-handed reliever Phillipe Aumont, pitching for the fifth time in five days, came on for the eighth inning. He retired Justin Maxwell on a fly ball for the first out. After walking Jason Castro, the Phillies caught pinch-runner Jordan Schafer stealing for the second out, extending the bullpen's scoreless streak to 21 innings.
Matt Dominguez drew the inning's second walk and Scott Moore reached after getting hit by a pitch. Manuel summoned Diekman, a lefty, to face the switch-hitting Lowrie, who took Diekman's second pitch into right-center field for the go-ahead double.
Manuel stood behind the decision to bring in Aumont for the eighth.
"That's what we wanted," Manuel said. "When he got on the mound, the more he stayed out there, you could see that he didn't have the stuff he had yesterday."
Aumont, called up from Triple-A Lehigh Valley on Aug. 20, had given up one run over his first 8 1/3 innings with the team. He pitched in both games of Sunday's doubleheader against the Rockies before tossing a scoreless inning Tuesday and Wednesday against the Marlins.
"I have to step up," Aumont said. "I did feel a little more tired than other days, but like I said, I've got to be prepared for those situations. For me, being new here, in those type of situations, it's something I've got to learn from and prepare myself better for next time."
Jonathan Papelbon was available in the bullpen, but Manuel wanted to save him for the ninth inning. The Phillies skipper was aware that Papelbon had pitched four times in the last four days and didn't know if he could get the final four outs.
Astros interim manager Tony DeFrancesco certainly didn't want to face Papelbon in the ninth.
"We knew if we didn't score there it would be tough in the ninth, but they battled through it," DeFrancesco said. "There were some guys throwing with some great arms, good velocity. We matched up nice and got a couple of big hits."
The Phillies held a 4-0 lead after three. Erik Kratz's double off starter Lucas Harrell scored Domonic Brown in the second. Juan Pierre, Chase Utley and John Mayberry all scored in the third.
The rest of the scoring came from the Astros.
Maxwell and Castro singled off Cloyd to open the bottom of the fourth. Dominguez followed with a three-run homer to the left-field boxes. Manuel decided to pull Cloyd after the homer, handing the ball to B.J. Rosenberg.
"I felt like [Cloyd] was having some problems," Manuel said. "It was time to get him."
The right-hander's fourth Major League start was his shortest. He threw 65 pitches, 43 for strikes, and struck out four.
Rosenberg, Josh Lindblom and Antonio Bastardo held the Astros to two hits over four innings before they scored three in the eighth off Aumont and Diekman.
After four runs through three innings, the Phillies managed just three hits. They loaded the bases in the sixth behind a single and two walks off Harrell, but Utley grounded out to first against reliever Xavier Cedeno.
In the eighth, Jimmy Rollins walked, moved to second on Juan Pierre's single and stole third on reliever Wesley Wright, who wasn't paying close attention to Rollins. It was the 400th stolen base of his career and 11th steal of third base this season.
Utley grounded out to second to end the inning.
Ryan Howard singled to open the ninth, but Mayberry struck out and Brown hit into a 3-6-1 double play to end the game.
"We have to score more runs," Manuel said. "Our offense has to produce more."