Steve Jones netted his eighth goal of the campaign but Crewe had to settle for a point after Gillingham hit back with David Perpetuini's long range effort in the second half.
It was no more than the Kent side deserved after an afternoon of hard endeavour which saw them take control of the game after the break.
Northern Ireland international Jones had given the hosts an 11th minute lead when he reacted quickly to volley in following a mistake by Gills keeper Jason Brown.
Under pressure from Chris McCready, Brown only managed to find Jones with his shot as he tried to punch clear David Wright's free kick.
Crewe were the sharper of the two sides in the final third of the first 45 minutes and with better finishing from Dean Ashton they could have extending their lead. Brown wasn't troubled by the striker's finish inside the box inside the 33rd minute.
Opposite number Clayton Ince had to be at his best to beat out Paul Shaw's first-time effort from eight yards out twelve minutes earlier after Nyron Nosworthy had centred from the right wing.
It was disappointing affair for a cold afternoon at the Alexander Stadium and it rarely got much better in the second period. Although the half started in explosive fashion when Perpetuini picked the ball up wide left of goal and hit a stunning drive 30 yards from goal which Ince failed to react to as it flew into his top corner.
Crewe withdrew the injured Ben Rix in the 58th minute and moved Anthony Tonkin up on the left wing, a switch which livened up their attacking ideas.
But Ashton blasted over a good chance from 20 yards after a neat build up between Tonkin and Kenny Lunt.
And the home forward failed to trouble Brown again in stoppage time with a good shooting opportunity to the right of goal but he pulled his low effort wide.
Paul Smith had earlier been given the chance to win the game when he was played in on goal by Shaw but placed his shot straight at him.