The Mariners had led 2-0 before and lost - two years ago in a nightmare finale against Brisbane Roar which was eventually settled by penalties. But not this time.
Dutchman Patrick Zwaanswijk, 38, the oldest player to appear in a grand final, gave the Mariners the lead just before halftime, powerfully heading home a corner from close range.
Daniel McBreen settled the issue with a superb penalty after Wanderers defender Jerome Polenz had handled in the box.
Try as they might, Tony Popovic's Wanderers could not fight their way back and give the rookie coach the victory his fans craved.
But they can still take pride in their remarkable achievement of winning the league title in their start-up year.
The Mariners also deprived Mark Bridge of an extraordinary treble, as he attempted to win a third grand final, all with different clubs.
-AAP