David Williams had earlier struck twice in six second-half minutes to put Melbourne seemingly in control.
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The deadlock was broken by Williams on 54 minutes, as he finished well one-on-one after being set up by Golgol Mebrahtu.
Williams doubled his tally on the hour, smashing a right-footed shot high into the net from close range.
The Mariners were given a route back into the match when Patrick Kisnorbo was penalised for pushing in the penalty area as both sets of players jostled for position at a corner kick.
Flores made no mistake from the spot, and the Argentinean was soon presented with another chance from 12 yards.
This time, Patrick Gerhart was the guilty party with a clear handball and, once again, Flores found the net with minimal fuss.
Williams looked poised to become the first player to score a hat-trick for Heart when he got on the end of Iain Ramsay's low cross late on. However, he was spectacularly denied by a superb point-black save from Justin Pasfield.