Brentford looked set to stretch their lead at the top of the table when they led at the break thanks to a fine David Hunt free-kick.
But Gillingham's top scorer, Simeon Jackson, earned his side a point when he scored from the penalty spot just before the hour-mark.
A draw was the right result as the teams cancelled each other out for long periods and good chances were at a premium.
A difficult pitch, strong winds and intermittent rain only served to make the game even less of a spectacle.
It did, however, have a top-quality first goal, scored by midfielder Hunt.
He curled a powerful 20-yard free-kick into the top corner four minutes before the break, leaving goalkeeper Simon Royce motionless, although he may have been out of position.
Jackson thought he had equalised seconds later when he slotted home after holding off Alan Bennett, but he was adjudged to have fouled the defender.
He did get a chance to level it up when his side was awarded a penalty after Andy Barcham skipped past Karleigh Osborne and was brought down by the defender's clumsy challenge.
Jackson made no mistake, drilling his spot-kick low to Ben Hamer's right but there were few other chances in an even game.
Gillingham's Mark Bentley cleared a Sam Williams header off the line and Charlie McDonald screwed a shot wide.
Mark McCammon headed wide when well-placed for the visitors and Jackson missed the target from 20 yards after beating a couple of defenders.
Sam Wood lashed a volley inches over for Brentford in the dying seconds, but the game didn't really deserve a winner and it didn't get one.