After a poor first half which saw the two teams struggle to muster a chance between them, the game burst into life in the second.
A Royce Brownlie strike just minutes after the restart seemed to have secured the points for the visitors, only for Mooney's late header to rescue a point for Wanderers.
A scrappy opening to the game saw neither team make an impact. Most of the action came from the crowd as Swindon's fans jeered their former striker Mooney.
The first opportunity fell to Wycombe after 12 minutes. Chris Palmer skinned his marker before finding Jermaine Easter, whose precise header was smartly turned away by Petr Brezovan.
With both teams looking devoid of ideas the first period ended with Swindon not even having had a decent attempt at Ricardo Batista's goal, and the fans praying for an improvement in the second half.
Things did, thankfully, pick up almost immediately, as, just six minutes in, Swindon took the lead.
Christian Roberts found Brownlie in space on the right and he attacked the goal and unleashed a low strike past Batista.
Swindon almost doubled their lead minutes later, with Roberts again the provider. He played in Fola Onibuje who looked to be one on one with the keeper, only for a fantastic last-gasp tackle by Will Antwi to prevent a certain goal.
Onibuje squandered another chance after 66 minutes, failing to find the target with a free header from Andy Monkhouse's free-kick.
Mooney had the chance to silence his critics and get his side back into the game on 74 minutes, but he shot straight at the goalkeeper from Jonny Dixon's pull back.
Wanderers never really looked likely to score, but, in stoppage-time, Mooney popped up at the far post to power home a header from Palmer's cross.