Odubel Herrera doubled twice and singled while Brad Miller hit a three-run homer as the Phillies averted a sweep and stopped Boston's four-game winning streak.
Wheeler (4-2) allowed only three hits in 7 1/3 innings, and retired 17 straight batters after a leadoff single. He matched the dozen strikeouts he had in 2013 for the New York Mets against San Diego.
''It popped into my head last night after the loss that we needed to get back on the right track and it comes down to me tomorrow,'' Wheeler said. ''I didn't put more pressure on myself. We needed to get back on the winning track going to Miami and keep it going. Hopefully, this starts a new little run for us.''
Philadelphia scored four times in the first off Eduardo Rodriguez (5-3). Rhys Hoskins singled home Herrera with the first run and after Alec Bohm walked, Miller hit a drive just inside the left-field foul pole for his fourth homer of the year.
''It was big today jumping out early and letting him cruise,'' Miller said. ''It's hard to throw a shutout every time. But when you have a little bit of a cushion, it allowed him to go into attack mode.''
Rodriguez gave up five hits and walked three in four-plus innings. He threw 103 pitches before departing two hitters into the fifth inning.
''I threw too many pitches,'' Rodriguez said. ''I have to work on that in the bullpen and keep going.''
Rodriguez did not pitch in 2020 after suffering myocarditis that was tied to his COVID-19 diagnosis. He has been trying to battle back and regain the form that had him 19-6 with a 3.81 ERA in 2019.
''We saw some flashes in the third and fourth innings of good mechanics and rhythm,'' Red Sox manager Alex Cora said. ''Mechanically, he started mixing his pitches better. The third and fourth inning, he was better. We'll take that as a positive.''
The first-inning run support was all Wheeler needed. Facing a Boston lineup that didn't feature Xander Bogaerts or J.D. Martinez - both given a day of rest by Cora before an off-day on Monday, Wheeler was able to mix his four seam fastball with a curveball that had Red Sox hitters on their heels.
''He was able to elevate his fastball and his two-seamer kept us honest,'' Cora said. ''We felt we put some good at-bats and put a good swing. But he's one of the best and he's very impressive.''
Only Franchy Cordero's long home run onto Ashburn Alley in deep right center to lead off the eighth blemished Wheeler's outing. Rafael Devers hit a solo homer in the ninth off Archie Bradley.
Wheeler improved his overall ERA to 2.38 on the season. He has been masterful at notoriously hitter-friendly Citizens Bank Park as well, going 3-0 in six starts with a 1.88 ERA, 52 strikeouts and just five walks in 53 innings.
''He's been important to us,'' Phillies manager Joe Girardi said. ''The thing is we have the full effect of him this year because he can swing the bat. He's gone deep into games and he's been great.''
Andrew McCutchen added a sacrifice fly and Herrera had an RBI double.
Herrera has made his case to fill Philadelphia's center field void, hitting .355 with two homers and eight RBIs in 62 at-bats since May 3.
Red Sox: Alex Verdugo was out of the starting lineup for the second straight game because of a left hamstring strain suffered in Friday night's win. He did come up in the ninth inning as a pinch-hitter for Marwin Gonzalez, grounding into a fielders choice. The Red Sox outfielder is expected to return on Tuesday against the Atlanta Braves.
Phillies: Bryce Harper was out of the Phillies starting lineup on Sunday as he continues to try to shake a 2-for-25 slump with 13 strikeouts in his last seven games with no hits in his last 16 at-bats. Harper has been bothered by a sore shoulder that was exacerbated last weekend against the Blue Jays.
''Just a day off,'' Girardi said.
Red Sox: After an off-day on Monday, the Red Sox will host the Braves to start a two-game set. Garrett Richards (4-2, 3.72 ERA) will get the start for Boston against Atlanta's Charlie Morton (2-2, 4.60).
Phillies: Philadelphia hits the road for a nine-game road trip that will start in Miami on Monday. Zach Eflin (2-3, 3.77 ERA) will start for the Phils against Marlins LHP Trevor Rogers (6-2, 1.74)
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