It was the first career triple-double for Carter-Williams, who had earned NBA Rookie of the Month honors earlier Tuesday.
His tie-breaking free throw in the second overtime put the 76ers ahead to stay and he later added a lay-in for a 123-120 lead.
The Magic's Aaron Afflalo poured in a career-high 40 points but missed potential score-tying 3-pointer in the final seconds of the second OT.
Glen Davis provided 33 points and Victor Oladipo also registered a triple-double of 26 points, 10 assists and 10 rebounds.
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