Played out on a bobbly pitch that offered little hope of quality football, this match was never destined to be a classic but both sides showed plenty of spirit to compensate for the poor conditions.
The visitors should have been in front after just three minutes as Tom Murphy found himself one on one inside the area but tamely chipped into the keeper's hands when he should really have done better.
Soon after Charlie Stimson was guilty of spurning a similar opportunity, while Dean Rance had a header saved by keeper Clement as the Gills squandered their early chances.
They were made to pay for their profligacy in front of goal as Aldershot took the lead with the last kick of the half. Carlton Cox collected the ball just outside his own area and fed George Landais inside the Gills half; he cut in from the left before curling a stunning 25-yard strike around Conor Quinn and into the far corner to give the Shots the advantage at the break.
Gillingham emerged stronger after the restart attacking with more urgency and showing better movement on and off the ball.
Still, they could not make their possession count and were thankful to centre-half Callum Davies for clearing Josh Pearson's deflected free-kick off the line.
Ten minutes from time substitute George Humber made a telling contribution, finding space on the right to cross for Dean Rance to volley into the roof of the net and bring the visitors level.
The equaliser knocked the wind out of Aldershot's sails and the Gills were on top of the game in the closing stages but still they struggled to fashion a winner.
Then in the 88th minute Charlie Stimson held the ball up on the edge of the box and was fouled from behind by Bergqvist. Stimson rolled the resulting set piece short to Rance who powered in his second of the afternoon to give the Gills a win.
There was still time for Stimson to earn an early bath, collecting a questionable red card in an off-the-ball incident which seems set to rule him out of the upcoming FA Youth Cup tie against Charlton.
Summarising events Manager Mark Patterson declared himself pleased with the teams display commenting, "We moved the ball as well as we could, and defended reasonably well in trying conditions.
"We scored two good goals that were worthy of winning any game, especially the first which was a tremendous strike. It was another hard fought win but, for me, those are the best kind."
Gillingham: Quinn, Bartrum, Essam, Davies, Evans, Geering (Benniman 55), Brunt (J.Brown 75), Rance, Stimson, Murphy, Day (Humber 65).
Subs not used: Hawkes, A.Brown.
