"We're playing good baseball and for me to get in there and contribute a little bit felt great," said Punto, who has been filling in for Pedroia while the former MVP recovers from a torn muscle in his right thumb.
"I've been telling him 'You'd better hurry up or I'm going to get you,' " Punto said. "We have a good time."
Punto had three hits and drove in two runs to lead Boston to its 10th win in 14 games. Daniel Nava also had two RBIs as the Red Sox (28-25) moved a season-high three games above .500.
Red Sox manager Bobby Valentine called Punto's performance "absolutely super."
"His timing at the plate was great today and it was really needed," Valentine said.
Punto's teammates gave him the silent treatment when he returned to the dugout after his first homer of the season, a second deck drive to right in the ninth. Valentine cracked up first, rising to his feet with a broad smile to give Punto an exaggerated high five.
"It was fun," Punto said. "I said 'Come give me some love. I've been playing this game a while but that's only my 15th home run, so come give me some love.' "
Doubront (6-2) allowed three runs, two earned, and seven hits in 6 1/3 innings, improving to 5-1 with a 2.72 ERA in his past five starts. The left-hander walked one, struck out seven and matched a career-high by allowing two home runs.
"Today he showed that he's a good pitcher because he was able to win the game without having his best stuff," Valentine said.
Doubront, who matched his longest start of the season, has not allowed more than two earned runs in any of his past five outings.
Catcher Jarrod Saltalamacchia called Doubront a "bulldog."
"Every start he's been solid," Saltalamacchia said. "It's the same thing every time. He doesn't trick anybody, he just has great stuff and good command."
Valentine said Doubront, a starter for the first time this season, has plenty of room for improvement.
"He's done great so far," Valentine said. "I think he's going to learn more about this league and learn more about himself and continue to improve. He's got a dynamite fastball."
Jose Bautista and Jeff Mathis each hit solo home runs for the Blue Jays, who have lost seven of 10 and fell into last place in the AL East. Eight of the past nine runs scored by Toronto, dating to Wednesday's win over Baltimore, have come on solo homers.
The Red Sox jumped on Blue Jays right-hander Kyle Drabek with a four-run, two-out rally in the second. Will Middlebrooks hit an RBI single, Punto doubled home a run and two runs scored when Nava's single dropped in front of center fielder Colby Rasmus, who appeared to misjudge the ball.
"It had top spin and it came back on him," Blue Jays manager John Farrell said. "It definitely had some movement back to his glove side."
Mathis answered for Toronto in the third with a solo homer that bounced off the top of the right field wall, his third, but the Red Sox made it 5-1 in the fourth when Kevin Youkilis doubled, took third on Bautista's throwing error and scored on Middlebrooks' double-play grounder.
Bautista, who flied out with men at first and second in the third, cut it to 5-3 when he homered to center to begin the fifth, his 13th.
Boston added an insurance run in the eighth. David Ortiz hit a one-out single and Saltalamacchia walked, bringing Francisco Cordero on to replace Darren Oliver. Youkilis walked to load the bases and Ryan Sweeney hit an RBI groundout.
An errant throw by Sweeney allowed the Blue Jays to score in the bottom half. With Edwin Encarnacion on first, Brett Lawrie grounded a single into right. Sweeney tried to return the ball to the infield but ended up throwing it behind second base, and was forced to chase it down himself as Encarnacion scored from second.
Drabek (4-6), who gave up a season-high nine runs in three innings at Texas last week, lost his second straight start. The right-hander allowed five runs, four earned, and six hits in 6 2/3 innings. He walked four and struck out four.
"Except for the second inning I'm happy with it," Drabek said. "I thought I was able to get some good strikes, quick innings and get our guys back in there."
Pedroia took batting practice before the game, the first time he has swung the bat since injuring his thumb last Monday. Pedroia has missed the past five games. ... Valentine said he would have put Pedroia in the game if SS Mike Aviles had been injured by a ball that hit him on the hand in the third. Aviles stayed in the game. ... The Blue Jays claimed RHP Chris Schwinden off waivers from the New York Mets and designated RHP Daniel Farquhar for assignment. ... Toronto RHP Sergio Santos (shoulder) threw 25 pitches from the mound during a bullpen session at extended spring training Friday and is scheduled to throw again Monday. ... Nava, who has made 23 straight starts, is expected to get the day off Sunday. ... Boston's Adrian Gonzalez started in RF but moved to 1B in the seventh. ... Attendance was 43,390, Toronto's biggest crowd since opening day.