Avery Bradley had 22 points and nine rebounds and Kelly Olynyk had 22 points in his fourth game back from a right shoulder sprain to help the Celtics even the season series with the Magic at two games each.
Boston led by 14 early in the fourth quarter and ended the game on a 9-2 run after having its lead cut to four. It was the Celtics' first home victory since their 14-game home winning streak was snapped on March 11.
Victor Oladipo led Orlando with 25 points and eight rebounds.
The Magic have lost four straight and eight of their last 10.
Injuries to key starters on both sides provided a different feel in the final matchup of the season between the teams.
Orlando's frontcourt was missing center Nik Vucevic, who has been out with a groin injury since March 7.
The Magic saw a different look from the Celtics as well, with starting forward Jae Crowder out for the fifth straight game because of a sprained right ankle.
The Celtics hit nine of their first 10 shots coming out of halftime to take their first double-digit lead of the night.
But Boston started 1 for 10 to begin the fourth quarter, allowing the Magic to quickly cut that deficit in half and get back into the game.
Boston came out sluggish, missing its first seven shots of the night. It also didn't help itself with six first-quarter turnovers.
Things changed after the Celtics began to push the pace and get easy baskets in transition. In one sequence that brought the TD Garden crowd to its feet late in second quarter, Thomas was able to find a streaking Bradley with a baseball pass for an easy layup.
It was two of 24 fast-break points Boston scored in the first half, compared to just 10 for the Orlando.
Magic: Vucevic missed his ninth straight game. Orlando is now 2-7 since his Vucevic's injury. ... Orlando dropped to 4-12 in the second game of back-to-backs this season.
Celtics: Boston has won 11 straight home games against the Magic. ... The Celtics improved to 10-6 in the second game of back-to-backs this season.
Boston hosts Toronto on Wednesday night.
Orlando continues its four-game road trip at Detroit on Wednesday night.
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