Clayton Donaldson had opened the scoring for the Bees but Zoko struck twice before the interval to turn the game on its head.
It was the visitors who came flying out of the blocks and they took a deserved lead on 13 minutes when Marcello Trotta released Jonathan Douglas, and his deft chip over advancing keeper Chris Day was forced over the line by Donaldson.
But just a minute later Stevenage were level when Bees keeper David Button dawdled on the ball and gifted it to Zoko who gratefully fired into an empty net.
Ten minutes later Jordan Burrow's shot from a Lucas Akins cross was blocked and Zoko was on hand to slot home the rebound.
Brentford were left shell-shocked and they never really recovered after the break although Donaldson did go close to an equaliser after 53 minutes but was denied by a fine Day save.