The Violets (11-1, 1-1 UAA) took their final lead of the game, 85-82, on junior Michael DeCorso's free throw with 1:53 left in the second overtime.
However, that was the last points NYU scored in the contest.
Following the free throw, the Tartans' Geoff Kozak tied the score with a three-pointer. Bary Dunn then gave Carnegie Mellon the lead on a layup with 39 seconds remaining.
After Carnegie Mellon's Greg Gonzalez made one of two free throws with 20 seconds left, making the score 88-85, DeCorso missed on a potential game-tying three-point attempt. Gonzalez grabbed the rebound and hit one more free throw with two seconds left to seal the Tartans' victory.
Carnegie Mellon (12-1, 3-0 UAA), ranked #19 in the most recent d3hoops.com poll, took it biggest lead of the game, 53-42, with 13:48 remaining in the second half. At that point, NYU produced a 24-7 run and took its biggest lead, 66-60, with 5:23 left.
Both teams had trouble at the foul line, with NYU making only 54.3% (19-35) and Carnegie Mellon only shooting 58.8% (20-34.)
The game featured 11 lead changes and nine ties.
Junior Jason Boone, who fouled out in the second overtime, scored a career-high 26 points for NYU. He also collected a game-high 14 rebounds.
DeCorso finished with a career-high 21 points, while senior Jared Kildare had 13 points and a game-high nine assists for NYU. Junior Chael Clark added nine rebounds and a career-high four steals.
Carnegie Mellon was led by Marques Johnson's 24 points. Clayton Barlow-Wilcox added 17 points and 10 rebounds.