Goals from Nikolai Topor-Stanley, Brendan Santalab and Youssouf Hersi sealed the victory for the away team, after Heart had equalised and then taken the lead through Orlando Engelaar and Jason Hoffman respectively.
Barring an extraordinarily heavy win for the Central Coast Mariners away to Brisbane Roar later on Saturday night, Tony Popovic's team will secure the runner up berth and enjoy a prized week off before entering finals fray with a home semi.
Heart meanwhile collect the wooden spoon as the competition's bottom team, having been unable to farewell retiring Socceroo great Kewell in a manner befitting his impressive career.
After both teams threatened in the opening 25 minutes, it was the Wanderers who drew first blood. Topor-Stanley, captaining the visiting team in place of Michael Beauchamp, connected with Shinji Ono's dipping free-kick to send a looping header over Tando Velaphi and into the back of the net.
Undeterred, Heart levelled the scores seven minutes later. Already involved in most of his side's good play without tangible reward, marquee midfielder Engelaar took matters into his own hands by unleashing a piercing long-range strike which flew into the corner of Ante Covic's goal.
Jonatan Germano threatened to become the villain of the piece for the home side when he was deemed, perhaps harshly, to have brought down Mark Bridge inside the area in the 67th minute. Ono however, usually so poised with the dead ball, blasted his spot-kick against the crossbar.
The Wanderers were made to rue their profligacy just minutes later, as the hosts took the lead for the first time in the game courtesy of Hoffman's deflected strike, the somewhat fortunate result of an ambitious driving run from the right-back.
In the 81st minute Western Sydney levelled, and there was an element of luck about the visitors' goal.
Fullback Jerome Polenz, played in behind the Heart defence, crossed to the centre of the penalty area. Substitute Santalab appeared to push centre-back Robbie Wielaert before hitting the back of the net, but the match officials were unmoved.
And the away team pounced again five minutes later, Heart failing to clear their lines and Hersi on hand at the back post to drill the ball to the far corner of Velaphi's net, ending the top-two hopes of rivals Central Coast and Melbourne Victory.
Melbourne Heart 2 (Engelaar 34', Hoffman 72')
Western Sydney Wanderers 3 (Topor-Stanley 27', Santalab 81', Hersi 86')
10,003 @ AAMI Park
