Wheeler (3-1) allowed three hits, struck out seven and walked one in his third straight win.
“I was throwing a good amount of quality pitches in there off-speed-wise and fastball-wise,” Wheeler said. “Command was a lot better today also. That was a big help.”
The right-hander was charged with seven runs in 11 innings over his previous two starts.
“The velocity and life to his fastball was as good as I’ve seen this year,” Philadelphia manager Rob Thomson said. “He was pumping strikes and using his secondary pitches - the sweeper, slider and curveball. He was really good.”
Nick Castellanos also connected for Philadelphia, and J.T. Realmuto had a sacrifice fly. Jake Cave had three hits, including an RBI single in the eighth.
Castellanos’ solo drive in the fourth went off the train tracks in left field.
Clemens greeted Phil Maton with his second homer in the sixth, a shot to right that drove in Realmuto. Clemens, the son of former Astros pitcher Roger Clemens - who was on hand for the homer - graduated from Memorial High School in Houston and played college ball at the University of Texas.
“He’s the same old, same old: ‘Way to swing it, kid. That a boy,’” Kody Clemens said of his dad’s reaction. “That’s the way he is.”
Kody Clemens said the home run was probably the top homer so far in his career.
“Obviously, my hometown,” he said. “A lot of family and friends here."
Jeremy Peña connected for the Astros in the eighth. He also went deep on Friday.
Houston slugger Yordan Alvarez had two hits in his return to the lineup after missing the last four games with neck stiffness.
“We’ve faced some pretty good pitchers the last few games,” Houston manager Dusty Baker said. “Like I always say, they ask me ‘What’s wrong with the offense? What’s wrong with the hitting?’ But on the other hand, everybody says hitting is the toughest thing to do in baseball. That good pitching beats good hitting.”
The Astros dropped to 6-9 at home this season.
Houston right-hander Cristian Javier (2-1) yielded three runs and seven hits in 5 2/3 innings.
Tempers flared in the fifth after Wheeler hit Martín Maldonado. Maldonado started walking toward the mound as he and Wheeler appeared to jaw at each other.
“I don’t know. I’m not him,” Wheeler said about being surprised with Maldonado's reaction. “Whether he thought I did it on purpose or not, it’s up to him how reacts to it. I think the only reason why we started talking to each other is because I saw his mouth moving and looking me, so I said ‘What’s up? You’re looking at me talking.’ That’s it. It was squashed after that.”
Realmuto and Mauricio Dubón, who was on deck, helped push Maldonado to first.
“The pitch was almost behind Maldy,” Baker said. “That was the perfect time to do it. Two outs, nobody on base. If he was trying to do it. Only (Wheeler) can answer that question.”
Maldonado was hit by a pitch from Seranthony Dominguez in the seventh, but he calmly took his base.
Kody Clemens was acquired by Philadelphia in a trade with Detroit for Maton’s brother, Nick.
Phillies: OF Cristian Pache was placed on the 10-day injured list with a torn meniscus in his right knee. Pache got hurt on Friday when he slipped going back to second base. Pache will have surgery on Monday. OF Dalton Guthrie was recalled from Triple-A Lehigh Valley to take his spot on the roster.
Astros: OF Chas McCormick (lower back tightness) started an injury rehabilitation assignment with Double-A Corpus Christi.
LHP Bailey Falter (0-4, 4.50 ERA) starts for the Phillies against Houston RHP José Urquidy (1-2, 5.64) in the finale of the three-game series on Sunday night.
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