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.
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.
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.
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, 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.
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.
