The teams met in the semifinals of the Global Sports Classic.
Cincinnati, ranked 20th in the country, found itself deadlocked with Iowa State at halftime and the Cyclones were within four with 1:52 left in the game after Will Clyburn hit a 3-pointer.
A Cincinnati turnover gave Iowa State a chance to get closer, but Korie Lucious missed a 3-point attempt and Kilpatrick followed with the first two of his four late free throws that gave the Bearcats some breathing room.
Kilpatrick made all 16 of his foul shots and scored 32 points. Cashmere Wright added 14 for Cincinnati.
Iowa State suffered its first loss of the campaign following four wins to begin the year. Tyrus McGee scored 22 off the bench to pace the Cyclones.