Mooney, who had missed the previous seven games with a hamstring injury, struck after 28 minutes as Walsall extended their unbeaten run in the league to 16 games.
The Walsall skipper also had a vital role to play at the opposite end of the pitch with a vital goal-line clearance from John Nutter in the 61st minute.
It was a timely intervention by Mooney as Walsall sealed their success 11 minutes later, when in-form Edrissa Sonko cut in from the right wing after good work by Lee Holmes to score his fourth goal in four games with a neat angled drive.
Andrew Crofts did gain the Gills some reward for their efforts with a spectacular injury-time strike from 25 yards, but it was no more than consolation.
The defeat leaves Gillingham, who have taken just one point from their last three games, too close for comfort to the relegation zone.
To avoid slipping any further down the table they need to find a cure for their travel sickness, as they have now won just twice in 13 games on the road.
Gillingham did open brightly but couldn't make their early pressure pay with Stuart Thurgood going close from long range and Mark Bentley seeing his shot charged down by Paul Boertien, following good work by Adam Miller and Nutter.
After a shaky start, Walsall finally got into gear and Holmes gave Gillingham a warning they failed to heed when his 20-yard free-kick was well saved by Derek Stillie.
But Stillie was powerless to prevent Mooney breaking the deadlock as the veteran marksman pounced after escaping from Ian Cox and Adam Bygrave.
Troy Deeney collected a throw-in from Rhys Weston and whipped in a right-wing cross that Mooney headed home from six yards.
Gillingham were fortunate not to fall further behind four minutes later when Mark Bradley's looping header, from a Holmes cross, crashed off the top of the bar.
Gillingham again made the early running in the second half with Gary Mulligan firing just wide, but the game swung on Mooney's goal-line clearance, as Sonko's strike moved Walsall into the thick of the promotion battle.