Halladay (2-1) missed his scheduled start last Saturday because of stiffness in his right arm. The 2003 AL Cy Young Award winner allowed one run and six hits, striking out two and walking one.
The Blue Jays needed Halladay to show he's healthy after placing Burnett on the 15-day disabled list with a right elbow injury earlier in the day.
"I felt great," Halladay said. "I didn't have anything like I had in the past. I'm excited going forward. I threw 90 pitches and felt good the whole time."
Halladay's velocity was down, but he said that was just rust. He worked on 12 days rest.
"He came back and threw strong. He wasn't as sharp as he usually is, but he had almost two weeks off," Toronto manager John Gibbons said. "He's fine. He's healthy."
The new-look Blue Jays are 4-1 against AL East rival Boston and have scored at least seven runs in each of those wins.
"I've been here four years and that is the best team they've had," said Red Sox slugger David Ortiz, who went 0-for-4.
The Red Sox have dropped three straight.
"When you go against a guy like Halladay the last thing you want to do is get behind," Boston manager Terry Francona said.
Reed Johnson and Wells singled in the first before Glaus doubled off the top of the wall in left -- missing a home run by inches. Molina followed with his homer to give Toronto a 4-0 lead.
"They hit balls with authority," Francona said.
Alex Rios' RBI infield single made it 5-0 in the second.
Rios followed with a sacrifice fly before Wells' two-run triple to left-center.
Wells went 3-for-4, raising his average to .397. The All-Star center fielder is off to a great start after having what he considered a disappointing season last year.
"It's great to see Doc back. It's unfortunate we lost A.J., but hopefully we'll get him back soon," Wells said.
- Burnett will visit Dr. James Andrews in Birmingham, Ala., on Monday. Andrews performed ligament replacement surgery on Burnett's elbow in 2003. Burnett, who signed a five-year, $55 million deal with the Blue Jays in the offseason after spending seven seasons with the Florida Marlins, began the season on the DL after scar tissue broke off in his elbow March 18 during spring training. The Blue Jays are hoping it's just scar tissue this time, too.