Australia will only have two representatives in this year's Asian Champions League after Melbourne Victory were defeated 4-3 in their qualifying playoff by an Andres Iniesta inspired Vissel Kobe.

Though twice able to overturn deficits and force extra-time in Japan, Victory were finally undone on Tuesday evening by a 95th-minute winner from Brazilian striker Lincoln.

That followed an early goal from Spanish icon Iniesta and a late brace from Yuya Osako.

It put a dampener on a star-making performance from Nicholas D'Agostino, who marked reports he is set to be called up for the Socceroos by scoring two goals and playing a major part in Ben Folami's dramatic 90th-minute leveller.

Victory's painful exit could also be the end of Robbie Kruse's season, the veteran attacker suffering a suspected ACL injury after coming off the bench in extra-time.

Kobe advance to the group stages of the ACL while Victory, unable to join Melbourne City and Sydney FC on that stage, will return home to face City in an A-League Men derby on Saturday.

His brilliance on show all evening, Iniesta took advantage of some poor defending to open the scoring in the sixth minute only for parity to be restored when D'Agostino bundled a corner over the line in the 12th.

Victory coach Tony Popovic was content for his side to sit back and play on the counter.

His strategy bore fruit in the 71st minute when they broke and Folami put a cut back on a plate for D'Agostino.

But Victory were made to pay for late wobbles in defence as Osako netted in the 80th and 87th to make it 3-2.

Yet more drama was to come when the ball fell to Folami after D'Agostino had a header saved and he curled an effort into the top corner.

Popovic, though, ran out of rabbits in his hat in extra time: Iniesta playing through Koya Yuruki to cut it back for Lincoln for the game's final act.