Mark Jackson's side had come back from a two-goal deficit and were looking good for a vital point with ten minutes remaining. Then a through pass was allowed to reach Daiju Sasaki just outside the area far too easily.
The striker took a touch then shot goalwards. The shot was straight at Dylan Peraic-Cullen who appeared to have it covered but somehow the shot burst through the keeper's hands and in, handing the Japanese champions a 3-2 win in Misaki Park Stadium.
The keeper could justifiably argue the ball should never have reached Sasaki, and he should have been more closely marked, but as the last line of defence keepers inevitably shoulder the blame.
The loss left Mariners one from bottom of the 12-team group, from which eight qualify, with one point from five matches.
With the last qualification place now six points distant they probably need to win all their remaining three matches. But they are against the teams currently third (Kawasaki Frontale), fourth (Yokohama F Marinos) and fifth (Johor Darul Ta'zim).
Kobe lead the east Asian standings with 13 points from their five matches, four clear of the chasing pack.
The hosts went ahead with Ryuho Kikuchi's 40th minute header. An own goal from Storm Roux four minutes after the restart looked to have settled the tie, but another own goal, by Hotaru Yamauchi in the 54th minute, gave Mariners hope.
Teenaged substitute Bailey Brandtman then levelled with 16 minutes remaining and Mariners looked good for a morale-boosting draw, only for Peraic-Cullen's 81st-minute slip to gift Kobe the three points.
Elsewhere on Tuesday Matias Vargas scored a hat-trick as 10-man Shanghai Port defeated South Korea's Ulsan HD 3-1, Japan's Frontale won 3-0 against Buriram United and Shandong Taishan claimed a 1-0 win over Johor.
Kevin Muscat's Port had been reduced to 10 men in the 31st minute when Li Ang picked up his second booking for pulling back Lee Chung-yong, but were already two ahead. Though Joo Min-kyu reduced the deficit in the 73rd minute Vargas restored Shanghai's cushion with seven minutes left.
That lifted the Chinese champions into eighth place, moving above Thai club Buriram on goal-difference.
Marinos, last season's runners-up, take on Pohang Steelers on Wednesday with South Korea's Gwangju FC, currently in second place, hosting Shanghai Shenhua.
with Reuters
