With the Rockets trailing 95-94, Harden threw an inbounds pass to Omer Asik, quickly got it back, and then drained a pull-up jumper from just inside the arc with 4.5 seconds left for the decisive score.
Harden finished with 29 points, including 15-of-17 from the free throw line, while also grabbing nine rebounds and distributing six assists.
Chandler Parsons helped out with 20 points and eight boards for Houston.
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