Striker Darryn Stamp broke the deadlock shortly before half-time after racing on to a George Boyd flick to lift the ball over the on-rushing Paul Jones in the Exeter goal.
As Exeter battled to find a route back into the game, Jon Nurse sealed the contest with 14 minutes left. Boyd's cross was palmed into the path of Nurse and the pint-sized striker drilled the ball past a stranded Jones to give Stevenage a vital three points.
Both sides knew the importance of this encounter as they battled to clinch a place in the end of season play-offs. The win lifts Stevenage back into the top five while the Grecians now find themselves six points adrift of a play-off place.
Exeter substitute Wayne Carlisle almost threw his side a lifeline in the closing stages with a thunderous free-kick, but City were out of luck and his effort cannoned off the crossbar and away to safety.
City will feel particularly aggrieved they could not snatch something from this crunch clash after dominating possession.
But a recent run of just seven points from their last 11 games has left their promotion hopes now hanging by a thread.
The Grecians will now have to dust themselves down for an FA Trophy semi-final showdown with Grays Athletic this weekend.
But for Stevenage this victory will ease the pressure on manager Graham Westley and revive their own promotion assault.