The Golden Eagles' Davante Gardner pulled Marquette into a 69-69 tie with an offensive rebound, a basket and a foul shot with 14.8 seconds remaining in overtime.
But Kilpatrick answered with a layup in traffic with 4.3 seconds left, and the Bearcats (16-3, 4-2 Big East) hung on for their third straight win when Junior Cadougan missed a short jumper at the buzzer.
Titus Rubles supplied a double-double of 12 points and 10 rebounds for Cincinnati.
Golden Eagles (13-4, 4-1), meanwhile, had their six-game winning streak snapped despite 19 points and eight boards from Vander Blue.
Gardner provided 15 and 11 for Marquette.