Danny Green added 17 points as the 76ers posted their third straight victory over the Celtics to sweep the season series.
The 76ers have won both games since Embiid returned from a 10-game absence while he recovered from a bruised bone in his left knee. They have won three of four overall.
Philadelphia led by 21 in the second half of the opener of a four-game trip.
Boston was trying for its first three-game win streak since early March. Jayson Tatum led the Celtics with 20 points, and Jaylen Brown finished with 17.
Boston had been inching closer to having its full roster available. That progress took a hit hours before the game when recent acquisition Evan Fournier entered the health and safety protocols.
The Celtics benefited from his presence in back-to-back wins over Houston and Dallas. His shooting ability from the outside helped create more spacing and forced opposing defenses to leave Tatum and Brown in single coverage.
Without him, Boston kept the ball moving Tuesday, but had trouble figuring out its rotations at times on defense.
Center Robert Williams, who has played some of his best basketball since joining the starting lineup six games ago, picked up two quick fouls in the first five minutes of the game and was forced to the bench.
Embiid seized on his absence and finished the opening period with 12 points.
Boston’s lack of success defending Embiid prompted coach Brad Stevens to insert 7-foot-5 Tacko Fall late in the first half and again early in the third quarter.
It pushed Embiid out of the lane, but he was able to pass out of double teams. He helped his teammates find their shot in the second quarter. Green had three 3-pointers and 11 points during a 15-0 run that put Philadelphia in front 52-37. Green was 5 of 6 from 3 on the night.