A Danny Jackman strike early in the first minute of the second half was enough to seal all three points for The Gills despite finishing with ten men.
Joe Martin picked up his second booking of the game, but it mattered not as The Gills clung on for their first win of 2012.
Andy Hessenthaler had the luxury of having just the one enforced change for the game with Jo Kuffour back at Bristol Rovers, meaning a return to the starting eleven for Lewis Montrose in a five man midfield.
Charlie Lee had to be content with a place on the bench alongside youngster Ashley Miller who was promoted to the sixteen man squad in Dennis Oli’s absence.
The game struggled to ignite in the first half and neither side got to grips with things early on. The only piece of action of note in the first 45 minutes was the booking of Joe Martin with barely a minute on the clock and it turned out to be crucial later on.
Garry Richards did force a save from former Charlton keeper Ross Worner, with Matt Lawrence, Danny Kedwell and Chris Whelpdale all spurning chances for the hosts.
With fans still finding their way back to their seats after the break, The Gills took the lead when Danny Kedwell and Curtis Weston danced around in the box before the latter laid the ball into the path of Jackman.
The diminuitive midfielder shifted the ball from his left to his right and then back again, dumping defenders on the floor in his wake before unleashing a shot low into the corner of the goal much to the delight of the Rainham End faithful.
Luke Guttridge had a great chance to reply for the hosts, but saw his header sail over when it seemed easier to score from Davies’ corner.
Then things turned for the worse for the home side on the hour mark when Martin picked up his second booking of the game as he mistimed a tackle on Jermaine McGlashan right in front of the tunnel.
The referee didn’t hesitate sending the Gills defender off, although he didn’t have far to trudge after picking himself up from in front of the advertising boards.
It was a case of siege mentality for Gillingham after that with Scott Davies denied by the ever alert Ross Flitney and the keepe was on top form to prevent Peter Vincenti from slotting the ball home.
Matt Lawrence was also on top form as he cleared Guttridge’s shot and in the end The Gills managed to hang on to what could be an invaluable three points come the end of the season.
FULL TIME: GILLINGHAM 1-0 ALDERSHOT TOWN
Gillingham’s fine win sees them maintain sixth spot in League Two and next up is the visit of Stoke City to Priestfield on Saturday for the FA Cup Third Round tie.
Gills line up: Flitney, Lawrence, Richards, Frampton, Martin, Whelpdale, Montrose, J Payne, Weston (Lee 83), Jackman, Kedwell.
Subs not used: Gazzaniga, Rance, Miller, S Payne.
Goal: Jackman (46).
Booked: Martin (2).
Sent Off: Martin (61).
Aldershot line up: Worner, Herd, Straker, Guttridge, McGlashan, Rankine (Smith 45), Rodman (Henry 85), Vincenti, Davies, Pearson, Doig (Brown 45).
Subs not used: Young, Day.
Booked: Smith (74).
Referee: Mr Chris Sarginson
Attendance: 5,432 (208 Aldershot).