Thanks to a late goal from skipper Travis Dodd, the Reds will now meet Asian champions Gamba Osaka.
Waitakere opened up the scoring in the 34th minute through Paul Seaman despite Adelaide having most of the possession but the lead didn’t last long.
Young defender Daniel Mullen powered a header into the back of the net from a Paul Reid corner just five minutes later.
The Reds then controlled much of the proceedings but it took them until the 83rd minute to eventually go ahead.
A glancing header from Travis Dodd proved the winner, knocking the New Zealand club out of the competition.
“We knew it was going to be difficult and they (Waitakere) certainly played very well. They made it very difficult for us, they were tight in the midfield and in defence and we were fortunate enough to get a goal with seven minutes to go,” Adelaide coach Aurelio Vidmar said.
“When they scored, I was still comfortable that we would be able to get back into the game and confident that we could do it. We just stuck at it and that’s what we had to do, we had to be patient.
“It has been a long time since we’ve gone into a game as clear favourites but that’s not a prerequisite of you just going out there and winning the game, it’s never easy. But the effort was there and we got the goals at the right time.”