Sam Gale scored his first Gillingham goal in the closing stages to end Crewe's perfect start to the season at Priestfield.
The centre-back flicked on a corner from Armani Little and then got into space, pouncing on a loose ball from close range in the 89th minute.
The visitors had the majority of the play early on and nearly took the lead when Mickey Demetriou's header following a Max Sanders free-kick came back off the crossbar.
The hosts, now unbeaten in 17, saw their best chance of the first half fell to Josh Andrews, who had initially chested down a long pass before finding Remeao Hutton. Advantage was played and the striker received possession back, but his effort from just over 18 yards went wide.
Crewe had a golden chance just shy of the hour when Josh March did well to control a long ball and get around the oncoming Glenn Morris. However, with the goal at his mercy, he missed the target.
Sanders went within inches of giving Crewe the lead minutes later, but his left-footed effort came back off the bar.
Gale converted from close range late on and was the first to react when Sam Vokes' header back across goal was punched away by Tom Booth.
Match report supplied by PA Media.
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