Coming into the NCAA tournament as a five-seed, Cornell flew past Hofstra and Princeton before upsetting top-ranked Virginia to reach the finals.
Looking to defend its national title, Syracuse easily slipped by Siena and Maryland before crushing Duke to reach the finals.
Senior Max Seibald put his team up 8-6 with less than seven minutes remaining.
With his team down 9-6 and less than four minutes to go, Syracuse sophomore attacker Stephen Keough scored his second goal.
Syracuse's Kenny Nims scored the goal to even the game with 4.5 seconds left and earned the tournament's most outstanding player honors.
Cornell won the faceoff to take the first possession in overtime but saw its luck end with a save by John Galloway in the Syracuse goal.
Senior Dan Hardy and his teammates celebrated after Cody Jamieson converted Hardy's assist at the 2:40 mark of the extra session for the game-winner.
Cornell and Syracuse came in even on almost every stat in a game that would feature 10 saves for each goalie and 72 shots.
Syracuse is the first to win back-to-back titles since Princeton won its third in a row in 1998.