Billy Clarke struck a minute from time to secure a point and atone for missing a penalty early in the second period.
Exeter – who are still in the hunt for automatic promotion themselves – took the lead just before the break when on-loan Charlton striker Stuart Fleetwood ran on to a throughball to round the keeper and slot home.
But the Bees took until the 89th minute to level when Sam Williams played in David Hunt to square for Billy Clarke to slot home at the far post.
His late leveller made up for a penalty miss four minutes after the break when City keeper Paul Jones got down well at his left-hand post to save.
Before the break Brentford looked likely to surge ahead with Jones tipping a Damian Spencer strike just wide – but Spencer later added to the Bees’ injury woes when he was forced off through a foot injury.