Shinji Ono set up Joey Gibbs to put the Wanderers in front in the 14th minute.
But Ryan Griffiths reacted quicker than team-mate Heskey to nod in James Brown's cross in the 27th minute and nine minutes later, Heskey showed great strength to reach Craig Goodwin's cross and finish with a deft flick.
Keeper Mark Birighitti preserved the Jets' advantage and they even survived the last-minute sending-off of Jacob Pepper for a bad foul on Ono.
Elsewhere, Melbourne Victory stunned Sydney FC with three late goals to steal a thrilling 3-2 win in a pulsating encounter at Allianz Stadium.
The Sky Blues looked to have buried the memories of last week's 7-2 loss to Central Coast Mariners when they went ahead 2-0 just after half-time - but substitute Andrew Nabbout's brace and Archie Thompson's strike turned the game on its head in the last 12 minutes.
Yairo Yau put Sydney ahead before a stunning volley from Pascal Bosschaart - the first goal of the Dutchman's 16-year career - doubled the lead.
But after Alessandro Del Piero was substituted in the 65th minute, the game turned around. Nabbout pulled one back with a thumping left-foot drive and headed an injury-time winner after Thompson equalised in the 86th minute.