Harden scored 16 points in the fourth quarter and overtime as the Clippers pushed their wining steak to five games despite the absence of star Kawhi Leonard with a sprained right ankle.
The Clippers trailed by 11 entering the fourth quarter, but Harden drilled a pair of free-throws with 1:24 left in regulation to tie it and after misses from both teams they went to the extra session.
Harden made four free-throws to open overtime as the Clippers pulled away, scoring eight of their 12 points in the decisive extra frame.
Scottie Barnes scored 24 points to lead seven Raptors players to score in double figures.
With their 12th victory in 14 games the Clippers have climbed into 10th place in the Western Conference, thrusting themselves into the post-season picture after a disastrous start to the season.
Evan Mobley threw down the game-winning dunk with 4.8 seconds left to play as the Cleveland Cavaliers edged the 76ers 117-115 in Philadelphia.
Three days after they were blown out by the Cavs, the 76ers were unable to turn the tables despite leading by as many as 11 points with 8:47 left to play.
Cleveland forward Jaylon Tyson, making a rare start with Darius Garland and Sam Merrill sidelined by injury, led all scorers with a career-high 39 points and fed Mobley for the game-winner.
Mobley scored 15 and Donovan Mitchell scored 13 points with nine rebounds and 12 assists.
Joel Embiid led the 76ers with 33 points. Tyrese Maxey added 22 but missed a half-court desperation heave at the buzzer.
In Brooklyn, the Nets squandered a 20-point fourth quarter lead before clawing out a 112-109 victory over Chicago that snapped their five-game losing streak.
The Bulls, trailing 92-72 with 11:20 remaining, had taken a 109-108 lead on Tre Jones's fastbreak layup with 11.4 seconds to go.
Michael Porter Jr. responded with a layup that put the Nets back on top and Noah Clowney sank a pair of free throws to seal the victory.
Porter led the Nets with 26 points and Clowney chipped in 23 points and 11 rebounds. Center Nikola Vucevic led the Bulls with 19 points.
"This is how a losing team becomes a winning team, learning how to win games like this," Porter said. "We're growing, we're getting better, so it's great."