The Rams (5-3) began the winning drive at their 22 with 3 minutes, 17 seconds left after the Crusaders (1-7) went ahead 32-29 on Ryan Laughlin’s 27-yard run and two-point conversion pass to Gerald Mistretta.
Koonce, who finished with 176 yards on 35 carries, scored to cap a drive that included 10 completions by Ryan Higgins, who was 38-for-56 for 407 yards and a touchdown.
Fordham led 23-10 after Patrick Murray kicked his third field goal on the first half’s final play.
Laughlin rallied Holy Cross to a 24-23 lead early in the fourth quarter with scoring passes of 24 and 9 yards to Mike Fess before Koonce’s second touchdown run gave the lead back to the Rams.
Fordham’s games don’t count in the Patriot League standings.