Melbourne City dispatched Floreat Athena 2-1 and Bentleigh Greens overcame Metrostars SC via penalty shootout after drawing 3-3.
In the big clash of the night at Campbelltown Stadium, it was Wellington Phoenix who took the initiative and burst into a two-goal lead.
Hamish Watson opened the scoring with a nice angled lob before Kosta Barbarouses doubled the advantage from an excellent Matthew Ridenton ball.
The Wanderers comeback was started by a superb performance from academy graduate Lachlan Scott, who, on debut, pulled one back before half-time and then equalised shortly after the restart.
The turnaround was complete when Mitch Nichols smacked in a long-range stunner to put Western Sydney ahead in the 70th minute, and that's how it stayed - Wanderers 3-2 winners to send Phoenix packing.
Meanwhile, in Melbourne, underdogs Green Gully pulled off an epic come-from-behind win of their own to eliminate Central Coast Mariners 2-1.
It was a sensational long-shot by Liam Boland, reminiscent of Danny Choi's effort from last week, well into injury time that sealed the memorable victory.
Elsewhere, in West Perth's Dorrien Gardens, Melbourne City progressed to the last 16 with a comfortable 2-1 win over Floreat Athena.
It looked like screamers were trend of the night, as Anthony Caceres produced his own exquisite strike to secure the result in the second half.
Finally, at the Elite Systems Football Centre in Adelaide, the scores were level 3-3 after extra time between Metrostars SC and Bentleigh Greens, so the tie was decided by a penalty shoot out where Bentleigh prevailed 4-3.