The win was the third straight for the Highlanders (9-8) and gave coach Jim Engles his 50th career victory.
Coming off an 83-78 triple-overtime win over Chicago State on Jan. 5, NJIT led by 16 in the first half and 39-25 at the break.
The Knights (7-10) opened the second half with a 9-0 run, keeping the Highlanders scoreless for more than 5 minutes, and took their only lead of the game at 52-51 with 6:07 remaining.
Tied at 60 with 1:21 left, Flores hit a jumper, then he and Woods made two free throws apiece in the final 19 seconds.
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