Sime Marnika scored 13 points and grabbed nine rebounds, while Jonathan Rosario and Cheick Fadika (seven rebounds) each added 10 points.
Baruch led by 20 points (40-20) early in the second half, but a 17-4 run by City College cut the lead to 44-37 with 10:14 remaining.
City pressed on and took advantage of some cold shooting by Baruch to further cut the lead to two points (50-48) with 1:50 left.
The Baruch defense then took over and driving lay ups by Garry Etienne (eight points, eight rebounds) and Rosario helped build a six point lead with 53 seconds left that was enough to kill the comeback and hold on for the victory.
The road win improves Baruch to 13-9 and 8-3 in CUNYAC. City College drops to 6-13 and 3-7 in CUNYAC.
The men will return to action on Saturday afternoon as they travel to the Bronx to face Lehman College. Tip off is scheduled for 2:30 p.m.