Goals either side of the break from Mateo Poljak and the returning Shannon Cole completed the historic aggregate semi-final victory following a goalless first leg in South Korea.
It means the fledgling club - founded in 2012 - become only the second Australian side to make the continental decider, following on from Adelaide United in 2008.
Tony Popovic's side will face Al Hilal of Saudi Arabia over two legs in the final, with the first match in Sydney on October 25, followed by the second leg away a week later.
The Wanderers couldn’t have dreamed of a better start as Poljak scored his first Champions League goal inside the first three minutes.
Seoul goalkeeper Yu Sang-hun punched Cole’s free-kick right into the path of the Croatian, who showed great control and awareness to keep his first-time volley down, finding its way through a slew of players and into the back of the net.
It took until the half-hour mark for Seoul to really get into the contest and their best chance of the half came 12 minutes before the break.
Antony Golec could only clear Kim Chi-woo’s cross into the path of Cha Du-ri and his deflected shot was headed towards the goal before Brendan Hamill cleared it to safety.
Chasing the away goal needed to see them through, the visitors lifted their intensity at the start of the second half but struggled to penetrate the well-structured and - at times - desperate Wanderers defence.
Cole's brilliant sliding challenge to block Osmar's effort epitomised the home side's commitment, and the Wanderers got the vital second goal through Cole in the 64th minute.
Labinot Haliti hung up a left-wing cross to the far post with Cole, who missed the first leg through suspension, outmuscling Chi-woo and diverting his header past Sang-hun.
The home side were then content to sit back and hold onto their lead, snuffing out any hope of a late Seoul fightback to continue their remarkable run in their debut Champions League campaign.
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