The win left Toronto (71-66) two games behind Boston (73-64). Each team has 25 games left.
"We expect improvement over last year, manager John Gibbons said, thinking back to his team's 80-82 finish last season. "Plus, if I'm not mistaken, there's playoff money when you finish in second place. So that ain't bad. There's a lot of trainers and some of those guys who could use that money."
The Red Sox, of course, had their sights set on first place in the AL East when they began August with a one-game lead over the New York Yankees. But Boston is 10-23 since then and trails the Yankees by nine games, its largest deficit since being nine behind on Aug. 17, 2004.
The Red Sox have finished second to the Yankees in each of the last eight seasons. They trail the Chicago White Sox by 6½ games in the AL wild-card race.
"It's really sad when your team thinks we can win the whole thing, but everybody got hurt at the same time," Boston shortstop Alex Gonzalez said. "It was pretty tough on us."
Gonzalez returned to the lineup after missing 15 games with a side injury, and catcher Jason Varitek and right fielder Trot Nixon were expected back Monday night against the White Sox. But the team's top two hitters, David Ortiz and Manny Ramirez, remain sidelined. Ortiz should be back soon after tests for heart palpitations showed no abnormalities. Ramirez has a sore knee.
With rain falling throughout, Chacin (7-3) got his first win since May 30 and improved to 4-0 against Boston, with three of the wins this season. He's pitched two strong games since struggling in his first game Aug. 23 after 2½ months on the disabled list.
"You've got to respect everybody in the big leagues and you've got to make good pitches to everybody," he said. "That's what everybody does, no matter who is in the lineup."
Josh Beckett (14-10) allowed his 33rd homer, a solo shot by Kevin Barker in the fourth, and lost for the fifth time in six decisions. He left after five innings, in part because he warmed up twice before the game because of the 1-hour, 8-minute rain delay at the start.
Chacin allowed two singles, one day after A.J. Burnett pitched a three-hitter in a 5-1 victory. Boston totaled 10 runs and 24 hits in the series and has scored three runs or less in 10 of its last 11 games. Its only run Sunday came in the ninth on Doug Mirabelli's RBI single.
"The hope is getting guys back gets players more into their suited roles," manager Terry Francona said. "Maybe it makes us a little bit better team."
Toronto had five doubles, two each by Molina and Gregg Zaun, after getting a season-high seven on Saturday.
Toronto took a 1-0 lead in the second on doubles by Molina and Zaun, then made it 2-0 in the third on doubles by Vernon Wells and Zaun.
Molina didn't change his approach because of the rain.
"I just try to still get my pitch, still try not to swing at bad pitches," he said. "If you change, you're going to find yourself in a hole, and to get out of there is going to be pretty tough."
Barker led off the fourth with a homer, his first since April 25, 2000, with Milwaukee at St. Louis. He has played just two major league games this season since being called up from Triple-A Syracuse on Thursday. His only other big league action since 2000 came in 2002, when he played seven games for San Diego.
Toronto scored twice in the sixth against Craig Breslow. The Blue Jays loaded the bases with no outs on Zaun's double and walks to Aaron Hill and Barker. Zaun scored on a wild pitch and Hill came in on Jason Phillips' sacrifice fly.
- DH Wily Mo Pena returned to Boston's lineup after missing eight games with a sore left wrist.
- Toronto 3B Troy Glaus and 1B Lyle Overbay didn't start because of illness but Glaus pinch hit in the sixth and struck out.
- Wells was ejected after striking out in the ninth.