Paul Pierce broke out of his series slump to score 27 points, and Rajon Rondo added 15 for the defending champion Celtics, who trimmed a 20-point deficit to seven before the Magic regained control.
Game 4 is Sunday in Orlando.
It was the second time this postseason the Magic won with a starter suspended.
Howard lost his cool and elbowed Samuel Dalembert in the head to draw a suspension for Game 6 of their first-round series against Philadelphia
- but Orlando still managed to get a blowout win and eliminate the 76ers.
This time, it was the Magic's big man who made sure a teammate wasn't missed.
The defensive player of the year had four blocks in the first half, forcing the Celtics into a jumpshooting team much like the Magic did to win Game 1. On the first play of the second quarter, Howard soared so high he had to brace his left hand against the backboard so he wouldn't smack his head, swatting Stephon Marbury's layup attempt into the stands.
It was no different on offense.
Howard sprinted down the middle of the lane to take a pass zipped from the wing by J.J. Redick, gripping the ball with two hands for a thunderous dunk that gave Orlando a 43-31 lead. The Magic would eventually go ahead by 14 points in the period.
But it didn't end there.
The Magic took a 20-point lead early in the third quarter before Howard picked up his fourth foul, and the Celtics ended the period on a 12-2 run capped by a breakaway dunk by Rondo.
The Celtics trimmed the deficit to seven in the fourth, and just when it appeared they would complete the comeback, center Kendrick Perkins lost his cool.