Milos Ninkovic and debutant Adam Le Fondre scored late to deny the Victorian NPL upstarts a place in the last four.

While rivals Western Sydney earned a 2-1 defeat of Melbourne City across town, the Sky Blues were pushed to the brink at a rowdy ABD Stadium.

FFA Cup specialist Liam Boland cancelled out Trent Buhagiar's first-half double with his own brace after halftime, igniting the 1566-strong crowd at Broadmeadows.

Buhagiar timed a far-post run perfectly to finish Le Fondre's fine work after 17 minutes.

The 20-year-old then finished through Avondale goalkeeper Chris Oldfield's legs after a superb through-ball from FC debutant Siem de Jong.

With five internationals on the pitch - and another, sick captain Alex Brosque - in the stands, Sydney had the pedigree and the professionalism to see off Avondale.

Instead, the state leaguers, through Boland, stepped up with two efforts; the first superb, the second opportunistic.

On 57 minutes, the towering striker was given too much space at the box and blasted home off the base of a post.

Until then, Avondale hadn't had a sniff. Then they came alive.

Boland was then on hand to poke home Andrew Redmayne's dropped cross just four minutes later as Avondale finished the stronger.

Despite playing 120 minutes on Friday to earn a place in the Victorian NPL final, they were all over the A-League powerhouses and twice forced Redmayne into fingertip saves.

But by extra-time, they looked shot, allowing Ninkovic to break hearts with a near-post finish and Le Fondre to score on debut with a breakaway effort.

New Sky Blues coach Steve Corica was a relieved man on the final whistle.

"I wouldn't say we got out jail but we got ourselves into trouble in the second half," Corica said.

"We were under the pump (but) once it went to extra time our fitness took over."

A Sydney derby looms large in the late stages of the competition after Wanderers' progression into the last four.

At AAMI Park, Markus Babbel earned the first A-League scalp of his short tenure as Wanderers coach with the visitors defeating City.

City should have gone ahead from the spot when Josh Risdon handled the ball in the box, only for Bruno Fornaroli to miss a 13th minute penalty.

Instead, the Wanderers surged with first-half goals to Oriol Riera and Roly Bonevacia.

Riley McGree rocketed home from a broken-down corner kick on 53 minutes, but City couldn't find an equaliser, ending their Cup run.

Australian Associated Press