Terry Antonis assisted Lachlan Scott's debut ACL goal before adding his own name to the scoresheet via a well-taken first-half penalty in Korea, before Jaushua Sotirio scored after the break to secure a first win by an Australian club in this year's tournament.
The win did not come without a late test of nerves though. Yun Il-Lok bagged a brace to put the defending K-League champions right back in it with nearly 20 minutes to play.
Both sides entered Wednesday night's group-stage clash armed with zero points and the knowledge that the loser could all but mathematically say goodbye to a knockout-stage berth.
The Wanderers, in stark contrast to their prior two dismal defeats, looked comfortable and pressed diligently on the rough pitch.
A rare 11-day turnaround would have helped, so too that Seoul were off their game for a good chunk of the contest - save for a bullet header from Montenegrin striker Dejan Damjanovic that rattled the crossbar early.
But the hosts' unhurried play from the back was soon punished when Antonis burst free and slipped a through-ball to Scott.
The hardworking 19-year-old, coach Tony Popovic's third striker in as many ACL games, finished instinctively with a helping hand from the post and goalkeeper Yoo Hyun.
The industrious Demjanovic took an immediate but marginally high stab at a long-range equaliser, but it wasn't long before Seoul were down another.
They had reason to feel aggrieved too, when Shin Kwang-Hoon was somewhat harshly adjudged to have handballed, but Antonis duly obliged from the spot.
Sotirio made it three just after the hour off a terrific Mitch Nichols through ball, but almost as soon as he'd lobbed over the on-rushing Yoo, Seoul awoke.
Yun wrongfooted Brendan Hamill and flicked the ball from an acute angle past Janjetovic at his near post.
He wasn't done there, soon nutmegging Kearyn Baccus in a superb finish from outside the area, as the hosts made the Wanderers work until the end.