Kevin Muscat's side opened the scoring through James Troisi's penalty, but fell behind by half-time after conceding soft goals to Sho Ito and Kosuke Nakamachi, with Shingo Hyodo appearing to put the game to bed when he netted in the 89th minute. Jimmy Jeggo got one back for the visitors in injury time, but it arrived too late for Australian side to mount a comeback.
The result sees Marinos join Victory on four points in Group G of the competition. Leaders Guangzhou Evergrande went down 1-0 away to second-placed Jeonbuk Motors earlier in the night, with those teams now level on seven points.
Victory, weakened considerably by their numerous absentees, might have anticipated finding themselves under pressure early in the game against a Marinos side badly in need of all three points.
Instead it was the visitors who started strongly, enjoying plenty of possession and then earning a penalty in the fifth minute when Hyodo tugged back Jason Geria inside the area. Troisi's well-taken spot-kick left goalkeeper Testsuya Enomoto with no chance.
In the 21st minute, despite previously only threatening intermittently, Marinos equalised in unusual circumstances. A hopeful long delivery forward saw the ball bounce off Leigh Broxham's back and fall kindly to Ito. Lawrence Thomas had come out to clear the danger, but the unexpected contact caused him to falter, allowing Ito to lift an exquisite chip over the stranded goalkeeper and into the unguarded net.
Six minutes later the hosts were ahead, and had a Thomas error to thank for the goal. The Victory custodian fumbled a high, whipped cross, forcing Broxham to try and clear the ball with an overhead kick. His attempt only got as far as Nakamachi inside the area, and the forward made no mistake in smashing home a fierce shot at the near post to make it 2-1.
Marinos dominated from the outset of the second half and should have had a penalty of their own two minutes before the hour mark. Geria gifted possession to Shunsuke Nakamura in a dangerous area and the former Celtic man wasted no time bursting into the area. His side-step left Adrian Leijer on the floor, before Leigh Broxham arrived to bundle over the former Japan international.
Appeals from Marinos players were waved away, but the incident sparked a flurry of openings for the home side.
On 61 minutes Jungo Fujimoto's cutback from the byline found Nakamura inside the area. This time a step over and burst of acceleration saw him tear away from both Leijer and Broxham, only for his shot to end up in the side-netting just outside the near post.
Two minutes later Nakamura, winding back the clock in a vintage performance, was involved again. His inviting corner reached Hyodo, whose shot struck the ground and sat up awkwardly, with Thomas required to tip the ball over the bar.
Still the chances continued to arrive, with Nakamura troubling Thomas from a long-range free-kick and finding himself at the heart of the Marinos' slick attacking football.
He went close again in the 85th minute, a carefully weighted lob attempt to the back post drawing a good save from Thomas.
In the last minute of normal time Archie Thompson went close to equalising, with his effort at the back post blocked by Enomoto and then scrambled clear.
Marinos' subsequent counter-attack saw Hyodo find himself in plenty of space on the edge of the Victory penalty area, and his opportunistic finish was well beyond the grasp of Thomas.
Not to be outdone in the counter-attacking stakes, the away side went straight up the other end and scored, Andrew Nabbout supplying the pass and Jeggo sneaking the ball beyond the onrushing goalkeeper.
There was no time to go in search of a third though, and Victory must now aim to beat defending champions Evergrande at Etihad Stadium on April 15 if they are revive their hopes of progressing to the last 16.
