The Bees started the match on top of the table, but looked to be heading for defeat after a terrible mistake from keeper Stuart Nelson gifted Neil Harris a goal on his debut for the Gills.
But young winger Ryan Peters, only playing because of an injury to Paul Brooker, headed an equaliser after the break to keep Brentford's spirits high.
The Bees should have taken the lead after only eight minutes when Peters sent Lloyd Owusu through on goal. But the striker's first-time shot was well saved.
Kevin O'Connor was also denied and Owusu wasted another great chance following good work from the lively Jay Tabb.
But Gillingham were always a threat with strikers Darren Byfield and Harris a constant threat.
Byfield really should have scored after racing alone on to a long goal-kick, and Harris claimed another shot had been handled off the line.
But the visitors did get the ball in the net eventually in bizarre fashion. There seemed to be no problems for goalkeeper Nelson deep in first-half injury time when he kicked a ball straight against Harris - allowing the former Millwall man to roll the ball home.
Gillingham continued to look strong after the break, with Matthew Jarvis outstanding.
But they conceded an equaliser in a barnstorming end to the game when Tabb crossed for Peters to head home at the far post.
Brentford could have won it through an Owusu header but a draw was the right result.