The win snapped a three-game losing streak for the Red Sox, who have the major's worst record at 3-10.
Travis Snider had an RBI single and stole a pair of bases for the Blue Jays. Toronto lost for the sixth time in nine games.
Lowrie, inserted into the leadoff spot to replace struggling outfielder Carl Crawford, went 3-for-5 to raise his average to .500. He had seen limited playing time, getting 17 at-bats before the start.
Beckett (2-1), coming off a dominant outing in which he shut out the Yankees with 10 strikeouts over eight innings in a win last Sunday, looked sharp from the start. He used a nasty curveball to go with his fastball to hold the Blue Jays to a pair of singles and a double. He struck out nine and walked two.
The 30-year old right-hander is coming off an injury-plagued 2010 season when he went just 6-6 with a 5.78 ERA.
Daniel Bard gave up a hit in the eighth and Jonathan Papelbon got the final three outs for his second save.
The Red Sox scored a pair of runs in the first, but it could have been more after they loaded the bases before Jo-Jo Reyes (0-2) got an out. Lowrie opened with a single, Dustin Pedroia walked and Adrian Gonzalez followed with an RBI single. Kevin Youkilis then doubled in a run, making it 2-0. After David Ortiz walked to load the bases, Reyes struck out a pair and got Darnell McDonald to ground out.
Reyes gave up four runs, seven hits, walked five and fanned three while throwing 94 pitches in four innings.
The Blue Jays cut it to 2-1 on Snider's RBI single in the second.
Boston made it 4-1 in the second when Lowrie homered into the Green Monster seats after Jacoby Ellsbury was hit by a pitch.
Notes
The 2-10 start had matched Boston's worst in club history, last done in 1996. They also opened 1925 and '27 by losing 10 of the initial 12. Crawford, off to a .137 start after signing a seven-year, $142-millon contract during the offseason, was taken out of the lineup for the day. "I think it'll do him a lot better to get a day off," Red Sox manager Terry Francona said. McDonald started in left and had a single in three at-bats. … Boston 1B Gonzalez made three diving stops on hard grounders by Corey Patterson. … Twenty-two years ago Saturday, Kelly Gruber became the first Blue Jays' player to hit for the cycle. … Fans lined the field on the warning track before the game as Red Sox players walked around and posed for pictures for about 45 minutes. … Blue Jays' SS Yunel Escobar had reached safely in 11 straight games, but went 0-for-4. … Toronto LHP Luis Perez made his major league debut.