Harry Forrester sent Coventry goalkeeper Joe Murphy the wrong way from the spot to net his second of the night after he was felled in the box by City defender Jordan Clarke.
The Sky Blues took the lead after seven minutes when David McGoldrick sprung the offside trap and ran on to fire beneath Bees goalkeeper Simon Moore.
But Uwe Rosler's side hit back just before the break when Forrester grabbed his first of the game when he slammed home after latching on to Adam Forshaw's through-ball.
Jake Bidwell's dipping free-kick midway through the half was palmed wide by Murphy at full stretch as Brentford pressed forward, but Paul Hayes missed two gilt-edged chances to put the game beyond doubt, first firing tamely wide when well-placed and then heading over when unmarked.
Brentford's inability in front of goal almost cost them when John Fleck's second-half screamer from 35 yards bounced to safety off the foot of the post.