Labinot Haliti's third-minute strike was all the Wanderers needed before showing all their defensive might and concentration to keep out the J-League giants.
The home side had to absorb pressure for large periods in the second half but held on for a crucial victory before a vocal crowd of just under 10,000 at Parramatta Stadium.
The win has pushed the Wanderers into second spot in the group, three points clear of Frontale ahead of the return fixture in Japan in a fortnight.
Wanderers boss Tony Popovic made nine changes to the side that played Adelaide on the weekend in an effort to freshen up his troops and they made the perfect start.
Kwabena Appiah played a clever ball in behind the Frontale defence giving striker Tomi Juric the perfect shooting opportunity just inside the box.
Juric failed to connect his effort with any great conviction but the ball squirmed right into Haliti's path for a simple tap in at the far post.
It was the third ACL match in a row the Wanderers had burst out of the blocks to go in front inside 10 minutes.
The goal seemed to spark the visitors into action and they could have equalised soon after.
Wanderers 'keeper Ante Covic failed to hold a speculative long range effort from Jun Kanakubo, only for Kobayashi Yu to blast the rebound into the side-netting.
Still trailing at the break, the J-League giants brought on Japanese international Kengo Nakamura and immediately gained the ascendancy.
Moriya Kentaro fired wide from close range while Yu was enduring a poor night in front of goal, squandering two opportunities in a couple of minutes.
Despite being on the back foot and starved of possession, the Wanderers still had their moments going forward.
Juric almost doubled the lead with a spectacular overhead kick which was heading in but for a brilliant fingertip save from Yohei Nishibe.
The visitors threw everything at the Wanderers in the dying stages but were met with body-on-the-line blocks and desperate clearances at every turn.
It won't go down as one of the Wanderers' prettiest wins but one of their most courageous and one which has given them a great chance towards the last 16 of the tournament.
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