The result sees the Mariners remain on six points and needing a win in Japan next week against Sanfrecce Hiroshima - along with other results to fall their way - to progress from Group F and into the competition's knockout stage.
FC Seoul weathered a series of good first-half attacks from the Mariners but couldn't convert their chances despite dominating large parts of the match.
And having missed their chances, the Mariners were caught by a late sucker–punch when John Hutchinson mis-timed a clearance two minutes into injury time and virtually passed a ball from Kim Jin-kyu into his own net.
Heading into the match, Mariners boss Phil Moss brought Hutchinson, defender Brent Griffiths, midfielder Kim Seung-yong and forwards Mile Sterjovksi and Matt Simon back into the starting eleven after they all didn't begin the match last weekend against Brisbane.
Choi Yong-soo made three changes for the Koreans after their scoreless draw against Gyeongnam last weekend, with former Celtic man Cha Du-ri, Choi Hyun-tae and dynamic midfielder Yun Illok given starting jerseys.
FC Seoul, though, have been struggling on the domestic front, having posted just one K-League Classic win this season from eight fixtures. They also hadn’t won away from home in six AFC Champions League games.
In an even opening, Mariners forward Simon and Brazilian Rafael for the visitor both had strikes on goal in the opening five minutes.
Sterjovski’s delightful turn in midfield then set up Joshua Rose tracking forward in attack, who saw three attempts denied from close range in a rapid-fire exchange.
Goalkeeper Kim Yong Dae was being kept busy as Mariners midfielder Kim and Simon had chances saved in the 14th and 17th minutes respectively.
Rose, however, was then exposed in defence later in the first half as Cha got in behind him to slam a shot into the underside of the crossbar.
Mariners goalkeeper Liam Reddy was equal to the task in the 32nd minute as Rafael struck hard while Kim Chi-woo also fluffed his line as Hutchinson nosed wide down the other end.
Four minutes before the break Nick Montgomery picked up a costly booking, his second of the competition – meaning he is suspended for the final group game.
Left back Griffiths also fired from long range late in the half, forcing FC Seoul’s Kim to save to his left.
Simon had a half chance to open the scoring in the second half before both sides called upon their substitutes, with Bernie Ibini injected for the locals and Go Yo-han for Seoul.
Simon, who had been treading a fine line all evening was replaced after he picked up a booking, making him the second Mariners player suspended for the trip to Japan for next Wednesday’s game.
A top-shelf Reddy save with his legs kept the game evenly poised after Escudero found himself in a great position following a delivery from lively replacement Go.
Reddy then pulled out a great save low to the ground before a Seoul produced a third chance in quick succession - this time from 22 year-old Yun, who missed a free header.
An almost untouchable Go beat the off-side trap after 68 minutes but Reddy saved at close range again.
Rose struck a rising ball, delivered by Storm Roux, with 14 minutes remaining in one of the Mariners best chances of the second stanza.
In a blow for the visitor’s, the energetic Go was forced off with what appeared a hamstring strain after barely 20 minutes on the park.
Ibini rushed a chance late for the Mariners, but Kim was untroubled in the FC Seoul goal.
After all their chances, a late delivery directed into the area by Kim Jin-kyu was turned into the Mariners goal by Hutchinson for what was deserved result for the visitors.
The reigning A-League title holders will now turn their focus to the A-League finals elimination match against Adelaide in Gosford on Saturday afternoon.
