A well-taken strike from Alou Kuol in the 14th minute gave the Mariners a first-half advantage at CommBank Stadium on Friday night before Ryan Edmondson doubled his side's lead.
James Temelkovski's 84th minute strike gave the Wanderers hope of mounting a late fightback but a breakaway goal from Mikael Doka ensured the Mariners went home with the three points.
The victory was crucial for the visitors, who risked losing touch with the top six after a slow start to their title defence.
"This is a really big win for us," said Mariners boss Mark Jackson.
"We knew the Wanderers were coming off some long travel from Perth and a short turnaround and we took advantage of that."
Mikael Doka scores the late sealer past Lawrence Thomas in the Mariners' victory. (Steven Markham/AAP PHOTOS)
Jackson's side have now picked up seven points from their past four games to rise to ninth, four points off the top six.
The Mariners are one point behind the Wanderers, who lacked creative spark in front of a home crowd of just 6,718.
Juan Mata watched from the substitutes bench until he was given a 20-minute cameo by Alen Stajcic, and in his short time on the field provided the pinpoint cross for Temelkovski to head in.
"I thought that was the best Juan has played," Stajcic said.
"He was creative and showed that extra bit of quality in the front third."
Finding a way for Mata to show his class has been an issue for the Wanderers all season but of more concern for Stajcic will be his side's defensive frailties. They have kept just one clean sheet all season.
South Korean centre back loanee Jeong Tae-wook was again absent through injury and Anthony Pantazopoulos was at fault for the Mariners' opener.
Nathan Paull floated a speculative ball into the Wanderers' box and Pantazopoulos was muscled off the ball by Kuol, who buried it past Lawrence Thomas.
The Wanderers goalkeeper survived a few scares in the second half and did well to parry a Doka effort away.
But Thomas was undone by his side's failure to clear a 69th minute corner on three separate occasions.
The ball was played back in towards Edmondson who finished past Thomas for his first goal since last season's grand final.
"It's the same with Alou, when strikers are in a spell and not scoring goals it's always a tough time for them," Jackson said.
"We need to help them by providing more opportunities and I thought we were more connected."
Mata's introduction provided the Wanderers some creative flair and Temelkovski was able to score.
Brandon Borrello went agonisingly close to drawing the Wanderers level, only for Harrison Steele to clear the ball off the line.
As the home side pushed for a late equaliser, Doka took off downfield and cooly finished past Thomas in the 94th minute to seal the win.
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