A red card to substitute Brent Griffiths and Tsukasa Shiotani's subsequent free-kick, deflected home by Satoru Yamagishi in the 72nd minute, cost Phil Moss and his team second place in Group F, with J-League champions Sanfrecce progressing as runners-up behind FC Seoul.
It was a cruel finish to a valiant campaign for Central Coast who, had they held on for a draw, would have booked an intriguing round-of-16 tie against Western Sydney Wanderers, the team that awaits them in the A-League semi-finals on Saturday evening.
A defensive-orientated Mariners, having packed the midfield and with Mile Sterjovski isolated up front, succeeded in frustrating their hosts throughout the first half at EDION Stadium.
Sanfrecce enjoyed two of their better chances as early as the third minute, before the visitors had a chance to settle into the contest. The openings fell to Naoki Ishihara from close range and then Hyung-Jin Park on the rebound, with Liam Reddy equal to the task on both occasions.
In the seventh minute Toshihiro Aoyama was set up by Ishihari's lay-off at the top of box and had Reddy at his mercy, but could only shoot over the bar.
Six minutes later it was Ishihari's turn to pass up a presentable opportunity, heading a half chance harmlessly behind despite giving the slip to Mariners centre-backs Eddy Bosnar and Zach Anderson.
The visitors' first glimpse of goal came in the 14th minute through Sterjovski, who hooked an awkward shot wide after some good work by Kim Seung-Yong.
It took until late in the half for either team to threaten again. On 40 minutes Yamagishi advanced into the penalty area, reached the byline and cut the ball back dangerously, with no team-mate able to get on the end of the inviting pass.
Three minutes later Shiotani stung Reddy's palms with a pile-driver of a free-kick from long range.
Sanfrecce went close again on 55 minutes, Park playing a good ball in behind the Mariners defence and Ishihara dragging a shot wide of the far post.
Two minutes later and a rare counterattack from the visitors ended with Kim firing wide of the target from range.
The hosts stepped up their efforts after the hour mark, Takahagi forcing an excellent save out of Reddy from a free-kick on 64 minutes.
Three minutes later and Sanfrecce wasted their best chance yet, substitute Koji Morisaki bursting into the area and shooting wide of the far post with Reddy beaten.
The pressure finally told in the 70th minute, when Griffiths, on for Bosnar only moments earlier, felled Ishihara just outside the penalty area with the forward through on goal.
The substitute was shown a straight red card for denying a clear goal-scoring opportunity and his team-mates were made to pay when Shiotani's free-kick was deflected off Yamagishi and into the back of the net.
Moss sent on Mitch Duke in search of a late equaliser, but the away side proved unable to worry Sanfrecce, who will now tackle the Wanderers on May 7 and 14 for a place in the quarter-finals.
