The loss dropped the Violets to 18-4 overall, 7-4 in the UAA and out of a tie for first place in the UAA, while the Yellowjackets (16-6, 7-4) moved into a tie with the Violets for second place.
NYU scored the first five points of the game, but an early 16-3 run gave Rochester the lead for good.
A three-pointer by junior Matt Basford brought NYU to within one, 25-24, with 4:27 left in the first half.
However, Rochester closed out the period on a 9-2 streak and took a 34-26 halftime lead.
After the Yellowjackets opened the second half by scoring the first five points, NYU never got closer than nine points the rest of the way.
Junior Jason Boone led NYU with 22 points, while senior Jason Kildare contributed nine points, seven rebounds and five assists.
Jeff Juron scored 18 points for Rochester, while Jon Onyiriuka added 16 points and 10 rebounds.