Paxton (2-2) allowed five hits in eight innings, struck out two and walked two, and Carson Smith pitched a perfect ninth.
"Just go after guys and make them prove they can hit the fastball. That's what I did today," Paxton said. "Everything felt pretty good. It was a lot of fastballs today. The breaking stuff is coming and just looking forward to the next one."
Paxton had struggled with his command early in the season while allowing 14 runs in his first three starts. Even in his previous start, when he pitched six innings against San diego, Paxton had trouble harnessing a fastball that regularly reaches 96 mph.
"It's no secret," Mariners manager Lloyd McClendon said. "Commanding the fastball, you're going to win. Makes everything better."
Boston put runners in scoring position just twice. Brad Miller snagged a hard hit groundball at shortstop from Dustin Pedroia to strand Blake Swihart at third base in the third inning. Swihart hit an inning-ending grounder with runners at second and third in the seventh inning.
Miller homered for the third time in two games, and Kyle Seager added a two-run drive in the eighth.
Steven Wright (1-1), starting in place of injured Justin Masterson, gave up three runs — two earned — and five hits in five innings.
Consecutive singles from Seager and Logan Morrison put runners on the corners with no outs in the second inning. Seager scored from third on a passed ball off Swihart's mask that went to the backstop, and Mike Zunino hit a two-out RBI single beyond the outstretched glove of Pedroia at shortstop.
Miller homered just inside the right field foul pole in the fifth for a 3-0 lead, his fourth home run in five games.
After Nelson Cruz walked in the eighth, Seager homered on the first pitch from Craig Breslow.
Robinson Cano has just four hits in his last 27 at-bats over the Mariners last seven games. He was 0 for 4 with two strikeouts against the Red Sox on Sunday and his season average has dipped to .253.
"Robbie Cano is one of the most unluckiest hitters in Major League Baseball," McLendon said. "He's really hit a lot of balls extremely hard that have been caught. I've not overly concered because he's not striking out a lot. I think when he gets hot, he'll get it rolling."
Red Sox: Masterson threw on flat ground before Sunday's game. Manager John Farrell said the inflammation in Masterson's right shoulder has lessened and he hopes to get Masterson back on the mound by midweek for some bullpen sessions before a rehab assignment.
Mariners: CF Austin Jackson went 2 for 4 for Triple-A Tacoma as he began a rehab stint Saturday night. Jackson has been on the disabled list since May 4 with a right ankle sprain. Jackson is expected to play the field for Tacoma for the first time on Sunday.
Red Sox: LHP Wade Miley (2-4, 5.60 ERA) will make his second-career start against the Texas Rangers on Tuesday. Miley lost his only decision against Texas despite allowing one run and three hits in 7 2/3 innings while with Arizona on June 13, 2012.
Mariners: RHP Taijuan Walker (1-4, 7.22 ERA) has held opponents to three runs or fewer in four of his last five starts.