The victory was the fifth straight for the Owls (9-2), who upset nationally ranked Villanova last Sunday.
The loss was the first for Seton Hall (8-1), off to its best start since 1988-89 when the Pirates went to the NCAA Tournament championship game.
The teams traded the lead nine times over the final 9 minutes before Scootie Randall's 3-pointer from the right corner broke a tie at 63 with 2:14 left. Brooks capped a clutch 7-0 run to make it 68-63 with 1:32 left.
Eugene Harvey, who paced Seton Hall with 16 points, cut the lead to 68-65 with 1:21 left. The Pirates had three shots to tie the game, but missed all three.
Fernandez iced the game with two free throws with 30.9 seconds left.