In the first-ever play-off encounter between the two sides, Le Fondre's 80th-minute header was the difference as the Sky Blues advanced to the last four.
They will host premiers Melbourne City next week in the first tie of a two-legged semi-final.
Their victory at CommBank Stadium came despite a boycott from their active supporter group, The Cove, and after the Wanderers had taken a first-half lead through a controversial Morgan Schneiderlin penalty.
Slovakian international Robert Mak pulled the visitors level in the 69th minute before Le Fondre escaped the attention of the Wanderers defence to grab a later winner off a corner.
Prior to Saturday Marko Rudan's side had lost just once after scoring first in the regular season, but the spirit shown by Sydney to fight back would have been encouraging for their boss Steve Corica.
The Wanderers had the better of the chances in the first half, skipper Marcelo flashing a close-range header wide and Milos Ninkovic forcing Andrew Redmayne into a fingertip save.
Calem Nieuwenhof helped get the breakthrough when he burst upfield in the 39th minute and attempted to send a low cross into the Sydney box.
Luke Brattan was able to block it with his foot but the ball cruelly bounced up and glanced Alex Wilkinson's upper arm.
Referee Chris Beath pointed to the spot and after consultation with VAR the decision stood.
Redmayne brought out his Wiggles-inspired theatrics but Schneiderlin remained calm and slotted it past the Sydney No.1 to hand the home side a 1-0 leading heading into the break.
Western Sydney were camped in their own half for the opening 10 minutes of the second half and rode their luck dangerously with Le Fondre and Paulo Retre both calling Wanderers goalkeeper Lawrence Thomas into action.
Eventually the Wanderers resolve cracked with Mak capitalising on a sloppy Adama Traore clearance to draw the Sky Blues level.
The loss of defender Tomislav Mrcela forced the Wanderers into a reshuffle and even though they pushed forward, it was Le Fondre who broke the deadlock.
The shortest man on the field for the Sky Blues, Le Fondre fizzed a header beyond the reach of Thomas to knock the Wanderers out.
20°C