Lin netted eight of his points in the fourth quarter, connecting on two jumpers to ignite a decisive 14-2 run.
The Knicks improved to 3-0 under interim Coach Mike Woodson and snapped a six-game road losing streak.
The Pacers got 24 points and 12 rebounds from Roy Hibbert but ended up on the short end for the sixth time in eight contests.
Paul George supplied 18 points and Darren Collison added 15 for Indiana.
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