The defeat dropped the Phillies to four games back of the second wild-card berth.
"Sooner or later you're going to get beat," manager Charlie Manuel said. "But at the same time that doesn't mean it had to happen tonight. We had a chance to win the game, it was sitting there in front of us"
Houston, 13-45 since the all-star break, won when trailing by four or more runs for the first time in 2012.
Aumont in the eighth was a winning formula until Thursday. He walked two and hit another. Fellow rookie Jake Diekman entered to clean the mess and permitted a two-run double to Jed Lowrie, batting for only the fourth time since July 14.
Manuel said Aumont "was out of gas" but stood by his decision to use him.
"That's what we wanted," Manuel said. "But when he got on the mound, the more he stayed out there, you could see he didn't have the stuff he had [before]."
The bullpen, once this team's weakest unit, enjoyed a renaissance until the fateful eighth. Phillies relievers had thrown 201/3 straight scoreless innings, including four more Thursday.
There was little support offensively. The Astros gifted two Phillies runs in the third inning. Before that, Erik Kratz snapped an 0-for-16 skid with a run-scoring double and Ryan Howard contributed a sacrifice fly.
That was all.
"It's a strange game," Howard said. "These things happen. It was a game we couldn't afford to lose, but they stuck in it."
Cloyd retired the first six batters in a row, three on strikeouts. Houston loaded the bases in the third but Cloyd escaped. It soured in the fourth when the first two Astros reached on singles and rookie Matt Dominguez launched a three-run homer into the short left-field porch.
Manuel sprang from the dugout as Dominguez crossed home plate.
"He was having some problems," Manuel said. "It was time to get him."
Cloyd was pitching on short rest and barely expended himself in 65 pitches. Before the game, Manuel was cryptic as to how long a leash Cloyd had.
Three runs, the Phillies decided, were too many in the heat of a September race. It marked the shortest outing by a Phillies starter since June 27, when Raul Valdes pitched two innings during a spot start.
A quick hook suggested the Phillies have little confidence in the 25-year-old soft-tossing righty. Cloyd dominated at triple-A Lehigh Valley and fanned nine Cincinnati Reds on Labor Day. More exposure has rendered him ineffective.
With the benefit of off days, it's possible Cloyd makes only two more starts in the season's final 18 games. The Phillies can skip one of his turns. His ERA in four starts is 4.95.
Ultimately, it fell upon Aumont, whose 23-year-old right arm has recently produced important outs. There was no such magic on this night.