Dean Saunders’ side trailed to Jonathan Douglas’s strike on the stroke of half-time.
It was a well-crafted goal that typified the enterprise of Brentford, with Adam Forshaw playing in the former Leeds midfielder who burst forward and deftly flicked the ball over Gary Woods.
Brentford were the better team throughout with their midfield completely dominant.
Saunders took off defender Shelton Martis on 56 minutes and threw Dave Syers into midfield, and that stemmed the tide.
Rovers got a way back in on 75 minutes when Cotterill scored with a lovely 25-yard drive into the drive into the far corner.
The goal lifted Rovers and with five minutes to go Tommy Spurr’s left-wing cross was met with a powerful header from an unmarked Paynter.
It was enough for Rovers’ third home win of the season.
Saunders said: “that result is just papering over the cracks. We’ve still got lots of work to do.
“Hopefully we can keep winning games while I sort it out.”