Dutch defender Patrick Zwaanswijk headed in the opener on the cusp of halftime and striker Daniel McBreen sealed the win at Sydney's Allianz stadium with a second-half penalty to dash the Wanderers' hopes of a dream finish to their debut season.
The Mariners celebrated wildly in front of a sell-out crowd of 42,000, having finally broken their drought after losing the competition's inaugural final in 2005-06, and twice more in 2007-08 and 2010-11.
"It's amazing. As I said to the fans a long time ago, this one's not for us. It's for them," Mariners skipper John Hutchinson, who played in all three of their losing finals, said in a pitchside interview.
"We've got some good characters here, some fantastic players. Some good youngsters as well, and before the game I just told them that this could be the last time that we play together as a team, so let's make it special."
The win was a triumph over adversity for the financially-stricken club from seaside Gosford, who at one point in the season lacked the means to pay their players.
Arriving in Sydney and branded three-times 'chokers' in the A-League's showpiece match, the Mariners confronted a sea of chanting, red-clad Wanderers fans in the stands and a nation largely backing their opponents.
The Mariners were the first to settle on a ragged pitch that had been used for a top-flight rugby match two days before and could have had their first goal in the fifth minute.
Bernie Ibini found himself unmarked in the box, but the Nigeria-born forward sprayed his shot into the stands.
Former Australia striker Mile Sterjovski came agonisingly close four minutes later for the Mariners when he delicately chipped over charging Sydney keeper Ante Covic, only for it to bounce off the crossbar and go behind.
Ibini had another clear shot in the 41st minute but struck it straight into Covic's arms.
The Wanderers, lacking talismanic midfielder Youssouf Hersi due to suspension, struggled to break down Central Coast's miserly defence but appeared set to ride their luck to the break before a costly lapse in defence.
Midfielder Michael McGlinchey sent an innocuous corner kick into the goalmouth where Zwaanswijk launched himself to head home from close range in the 44th minute, picking the perfect time to score his first goal of the season.
Wanderers fans again howled in dismay a minute later when Mariners fullback Pedj Bojic stopped the ball with his arm in front of goal, but referee Peter Green waved away appeals for a penalty.
Sydney defender Jerome Polenz enjoyed no such leniency from Green in the 67th minute and was penalised for handball in the box. Man-of-the-match McBreen coolly drilled the spot kick home to put the Mariners on the verge of victory.
The shell-shocked Wanderers scrapped hard to try to find a way back but could not fashion a clear path to goal, with former Japan playmaker Shinji Ono shackled well by the Mariners throughout.
Ono had his team's last genuine chance with six minutes left on the clock, but his free kick from outside the box sailed well over the goal.
The loss was a bitter pill to swallow for the Wanderers, who were unbeaten in their previous 13 matches and had collected the Premier's Plate by leading the standings at the end of the regular season.
"It's been a crazy season for us and I definitely don't believe this one game defines it," Wanderers skipper Michael Beauchamp said at the post-match presentation.
"A credit to our boys, we gave it right up to the last minute and you can't ask for anything more than that."
The match capped a positive season for Australia's fledgling soccer competition, which has struggled to prop up a number of insolvent clubs since its inception in 2005, in a market dominated by Australian Rules football and rugby league.
The A-League garnered international headlines and unprecedented interest with the recruitment of former Italy great Alessandro Del Piero by Sydney FC, along with former England striker Emile Heskey (Newcastle Jets) and Ono.
The Wanderers' fairytale run did the most to capture the country's imagination, however, the team having been just a concept a little over a year ago, lacking colours, fans, a coach and players.
On-field success crafted by manager Tony Popovic and a well-drilled staff quickly built a passionate following in Sydney's unfashionable west, and the Wanderers came one match shy of rewarding their loyalty with the competition's ultimate prize.