The Raptors (22-20), meanwhile, got their first road victory since beating the Washington Wizards on Jan. 3. They also improved to 3-0 against the Sixers this season.
In the process, DeMar DeRozan continued his dominance over the home team.
The 6-foot-7 shooting guard is averaging 31.3 points against the Sixers after posting a game-high 34 points on Friday night.
DeRozan has scored 74 points in the last two games. He produced a career-high 40 against the Dallas Mavericks on Wednesday.
On Friday, the Southern Cal product scored 16 in the fourth quarter. His first seven of the quarter gave the Raptors some breathing room.
"When it's time, my team turns to me to win the game, to be honest," he said. "That's my job: to go out there, close the game, and try to lead us to a victory."
Down by 82-78, the Sixers opened the quarter by sandwiching two missed baskets around a turnover on their first three possessions. DeRozan then responded by scoring the Raptors' next seven points on a dunk, a three-pointer, and a 17-foot jumper to give them an 89-83 cushion with 8 minutes, 33 seconds left. The jump shot started a 9-0 run gave Toronto a 13-point lead with 4:47 left.
DeRozan later iced the game with four late foul shots.
"It's fair to consider him an all-star," Sixers coach Brett Brown said.
Raptors point guard and Villanova product Kyle Lowry finished with a triple double, with 18 points, 13 assists, and 10 rebounds in the Philadelphia native's return home.
"There used to be a point where the Toronto Raptors walk in and you're like 'OK, this could be an easy one,' " said Sixers power forward Thaddeus Young, who finished with 16 points, 7 rebounds, and 3 steals. "We know they have a lot of key guys on that team. They can do a lot of different things. "Tonight, DeMar was big for them. Kyle Lowry was big, also."
Rookie point guard Michael Carter-Williams led the Sixers with 20 points and five assists. Spencer Hawes added 14 points and 12 rebounds.
Sixers backup point guard Tony Wroten missed his third consecutive game with a sprained right ankle.
"Tony will go . . . maybe tomorrow, but a little bit longer than I had expected," Brown said of Saturday's game against the Oklahoma City Thunder at Wells Fargo. "That's fine. If that's what his body is telling me, and that's what the doctors are saying, then so be it. We will get him back at full strength when he's ready."