Reserve Ryan Anderson scored 20 to lead the Magic, who survived another slow start and spotty defense with some big baskets down the stretch.
Lou Williams led Philadelphia with 19 points and Thaddeus Young had 17.
At Wednesday morning's shoot around, Magic coach Stan Van Gundy said playing better defense and getting off to a fast start were his team's focal points coming off a mediocre 2-3 road trip.
Sixers coach Doug Collins said he wanted his scrappy team to play loose against a team that had changed dramatically since their 97-89 win over Orlando back on Dec. 18.
It took until the final moments of regulation and the extra frame, but what the Magic couldn't provide with another slow start and spotty defense, they made up for with late-game toughness. Orlando sprinted out to a 95-92 advantage in overtime, before back-to-back baskets by Andre Iguodala put the Sixers back up 96-95.
J.J. Redick was then fouled on a 3-pointer and hit his free throw to put the Magic back up 99-96 with 1:44 left. Young scored to trim the lead to 99-98 with 43.4 left. But after a miss, the Magic won a scramble for the ball to secure the win.
Trailing 70-63 entering the final quarter, Orlando picked up its defense, forced some quick shots and scored seven straight points to pull within 72-71 with 9:59 to play. Two free throws by Howard a few trips later gave the Magic a one-point lead with at the 9:29 mark.
Hedo Turkoglu's basket tied it, before Iguodala's fade away made it 86-84 with 1:04 to play.
Howard fouled out going for a rebound on the Magic's next trip and after a technical free throw by Williams for a delay of game, the Sixers got the ball back with 49.4 seconds left.
Iguodala was fouled by Brandon Bass on a layup attempt and hit a pair of free-throws to make it 89-84. A free throw by Williams made it 90-86. But on the next trip he fouled Richardson on a 3-pointer, and Richardson completed the play at the line.
NOTES: Orlando allowed opponents to score 100 or more points three times during its five-game road trip ... Philadelphia won the last meeting between the teams 97-89 loss on Dec. 18. ... The Sixers had won two straight.