Tomi Juric and Youssouf Hersi secured victory with their first-half strikes, ensuring the Wanderers remain the only side still unbeaten at home this season.
The win, in front of 15,786 boisterous fans, lifted them to within just two points of top-placed Brisbane on the ladder while the Mariners slide to sixth.
Having gone down 2-0 to the Mariners last time the sides clashed at Pirtek Stadium, the Wanderers were determined to reverse the result.
Juric showed he hadn't lost his deft touch in front of goal after five weeks on the sidelines, breaking the deadlock in the 20th minute with a classy volley.
Already the club's top scorer, despite having missed half of the Wanderers' games this campaign, Juric added to his tally with his fourth of the season.
The young striker, who is hoping to get on Socceroos coach Ange Postecoglou's radar, moments later got past two defenders to draw a save from Liam Reddy and remained a constant threat throughout.
Livewire winger Hersi doubled the advantage in the 33rd minute courtesy of a pinpoint cross from Shinji Ono to ensure the Wanderers bettered their recent goal-scoring record, having netted no more than one goal in their past six encounters.
Matthew Spiranovic may also have strengthened his claims for a Socceroos spot and has ensured skipper Michael Beauchamp faces an uphill battle to get back in to the Wanderers' squad with another impressive display in the centre of defence.
Spiranovic cleared a shot off the line by Mariners playmaker Marcos Flores in the first half and was a menace in defence.
Flores' wasn't the only chance for the defending champions, with All White Michael McGlinchey, Joshua Rose and Nick Fitzgerald also threatening.
The Mariners started the second half desperately trying to claw their way back into the game.
Coach Phil Moss brought on striker Mitchell Duke for Flores with half an hour to go and the 22-year-old was dangerous from his first touch, forcing a save from Wanderers keeper Ante Covic just moments after coming on.
In an effort to get more firepower up front, Moss replaced veteran Daniel McBreen with Matt Simon in the dying minutes, but to no avail.