Chris Beardsley grabbed a deserved winner for Stevenage as Brentford were booed off by their own fans.
The striker reacted quickest to a loose ball to lash home the only goal of the game from 12 yards.
Brentford, who are now two points above Boro, created just two real chances, Niall McGinn driving over and Miguel Llera heading straight at Chris Day.
And they were punished by Beardsley as Stevenage recorded a first league win over their opponents.
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Stevenage manager Graham Westley told BBC Three Counties Radio:
"It's good to get another clean sheet. We're disappointed with the way we've defended this year so far.
"We've not been the best defensively this year, we know that, but we're taking strides to put that right.
"It was a strong professional away performance."