The game was the season opener for the Blackbirds, Loyola-Maryland entered after a season opening loss to Tennessee State on Friday.
The score was tied on three separate occasions over the final three minutes, and neither team held a lead greater than two points.
Aakim Saintil hit a jumper for Brooklyn which gave the Blackbirds a 68-66 lead with 1:02 left. After a foul by Saintil on the ensuing possession, Andre Walker stepped to the line and drilled a pair of free throws to tie the score at 68 with 43 seconds left, setting up Hernandez' final play heroics.
Martin Hermannsson finished with 14 points for the Blackbirds.
Jarred Jones led Loyola-Maryland (0-2), with 18 points.