Second-half goals by Paul Shaw, his third in a week, and youngster Danny Spiller earned Gillingham their third win in four games.
Shaw broke the deadlock just past the hour mark with an excellent strike to beat the impressive Clayton Ince, and then Spiller's excellent diving header secured the points.
Crewe finished with ten men with midfielder Kenny Lunt earning the Railwaymen their first red card of the season following an 82nd minute tussle with Gillingham player-manager Andy Hessenthaler right in front of the dugouts on the halfway line.
It was a deserved victory for the Gills who dominated the first half.
Shaw was denied a 20th minute opener by a good save from Ince, who then saved again from Spiller a minute later.
Crewe's Dean Ashton might have done better when he shot straight at Jason Brown midway through the first half and Gillingham might have had a penalty when David Perpetuini looked to be taken down in the box by Neil Sorvel.
Then a Lunt free-kick bounced across the face of the Gillingham goal, before Ashton ballooned another effort high over the bar in first-half stoppage time.
Both teams upped the tempo in the second half. Nicky Southall drove over from 25 yards and then Ashton headed against a post.
However the turning point came when Brown pulled off a fine save to deny Steve Jones and a minute later the home side broke away and Shaw gave them the lead.
He got free of his marker in the box before drilling a low right-foot shot wide of Ince and into the far corner.
Hessenthaler made it with a low ball into the area with the Gills player-boss having one of his wholehearted and competitive afternoons.
Then Spiller produced a perfect finish to convert a Nyron Nosworthy cross as the Gillingham utitilty man, starting the day at centre-half alongside Barry Ashby, popped up on the left wing.
Lunt got his marching orders for two yellow cards with Anthony Tonkin and Ashton also booked.
The only downside for Gillingham was that the game attracted their lowest crowd of the season, less than 7000, but nine points out of 12 had lifted them into a comfortable mid-table position, despite the squad being severely tested by injuries and suspensions.