The midfielder had only been on the field 69 seconds when he struck at the start of the second half to seal three valuable points for Gary Megson's side.
Wanderers' third successive home win moved them up to tenth in the table and left the Magpies in a perilous position just three points above the relegation zone.
Johan Elmander very nearly gave the hosts a dream start on ten minutes but the Swede's effort was cleared off the line by Jose Enrique.
Bolton were unfortunate not to be awarded a penalty minutes later when Kevin Davies was bundled over in the area by a clumsy challenge from Sebastien Bassong, but referee Alan Wiley waved away the protests.
It was all Bolton in the early stages and Elmander really should have done better than fire over from six yards from Matt Taylor's inviting low cross on 19 minutes.
Newcastle did hit the upright but Bassong's header would not have counted after the defender was penalised for a foul.
The visitors gradually began to take control and Nicky Butt and Peter Lovenkrands would have both been disappointed not to have done better when well placed.
Obafemi Martins and Jonas Gutierrez then forced a saves from Jussi Jaaskelainen as the Magpies surged forward in search of the game's opening goal.
Martins went close again but the striker headed just wide from Gutierrez's cross while, at the other end, Elmander squandered another fine chance on the stroke of half-time.
Gardner replaced Fabrice Muamba at the start of the second half and he needed less than 70 seconds to make his mark when he swept home Matt Taylor's cross after fine Bolton move.
Newcastle tried to hit back immediately and Ryan Taylor curled an effort on to the roof of the net.
The former Wigan player then fired a free-kick over from a promising position after the dangerous Gutierrez had been upended on the edge of the penalty area by Gretar Steinsson.
Shola Ameobi forced a fingertip save from Jaaskelainen on 77 minutes and, just a minute later, Newcastle should have had a penalty when Jlloyd Samuel clearly blocked Fabricio Coloccini's goal-bound drive with his hands.
But Wiley turned down the appeals and with it went the visitors' hopes of salvaging a point.