Reliable skipper John Hutchinson cost his team all three points by putting through his own net in injury time after the hosts had looked set to survive a second-half onslaught
The result leaves the Mariners on six points and needing a win in Japan next week against Sanfrecce Hiroshima, and the other result to fall their way, to progress to the knockout stage.
Seoul weathered a series of good first-half attacks from the Mariners but could not convert their own chances despite dominating large swathes of the match until the late winner, when a delivery from Kim Jin-kyu was directed into the back of the net by Mariners captain John Hutchinson, who had dropped back into defence after a late enforced re-shuffle.
Phil Moss returned Hutchinson, defender Brent Griffiths, midfielder Kim Seung-yong plus forwards Mile Sterjovksi and Matt Simon to the starting XI, making five changes, the captain and Simon having missed the 2-0 win over Brisbane Roar last weekend.
Choi Yong-soo made three changes for the Koreans after their weekend scoreless draw against Gyeongnam with former Celtic man Cha Du-ri, Choi Hyun-tae and dynamic midfielder Yun Il-lok given starting jerseys.
FC Seoul are struggling on the domestic front with only one K-League Classic win this season in eight fixtures and hadn't won away from home in six AFC Champions League games.
Simon for the Mariners and Brazilian Rafael for the visitors both had strikes on goal in the opening five minutes.
Sterjovski's delightful turn in midfield set up Josh Rose, who was denied with three attempts from close range in a rapid-fire exchange.
Goalkeeper Kim Yong Dae was kept busy with Kim, via a free-kick, and Simon after 14 and 17 minutes respectively enjoying good chances.
Not for the first time Rose was exposed in defence as Cha got in behind to slam a shot into the underside of the crossbar but the ball didn't fall kindly for the visitors in their best first-half chance.
Mariners goalkeeper Liam Reddy was equal to the task in the 32nd minute when Rafael struck a hard effort from Choi's cross.
Both skippers got involved in the attacking action moments later as first Kim Chi-woo then Central Coast's Hutchinson, again from a Kim free-kick, just glanced a header wide to the left.
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.
Defender Griffiths' shot from range late in the half then forced Seoul's Kim to save to his left.
Simon had a half chance to open the second term before both sides called upon their substitutes, with Bernie Ibini injected into the game for the home side and Go Yo-han for the K-League side.
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 even after Escudero was in great position following a delivery from lively replacement Go.
Reddy pulled out a great save low to the ground again before 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 and Reedy 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 visitors, energetic Go after barely 20 minutes on the park came off with eight minutes remaining, troubled by what appeared to be a hamstring strain.
Ibini rushed a chance late on for the Mariners and Kim was untroubled in the Seoul goal.
After seeing all those chances somehow missed, it was a late delivery directed into the area by Kim Jin-kyu and turned into the Mariners goal by Hutchinson which decided the game in the visitors' favour.
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.
FC Seoul 1 (Hutchinson (og) 92)
Central Coast Mariners 0
Crowd: 4,118 @ Central Coast Stadium