A goal apiece from Darryn Stamp and Jon Nurse either side of half time handed Stevenage a major boost in their push for a Conference play-off place.
The hosts dominated the opening stages but failed to capitalise and were punished on 38 when Stamp strolled through to fire home the opener.
Exeter rarely displayed their early promise after that but Stevenage had to wait until the 77th minute to seal it.
Jon Nurse fired home to give his side a vital win over their promotion rivals.
Exeter: Paul Jones, Woodards, Sawyer, Todd, Billy Jones,
Taylor (Carlisle 79), Cronin, Buckle, Challinor,
Flack (Gill 79), Farrell (Edwards 66).
Subs Not Used: Rice, Gaia.
Stevenage: Julian, Henry, Goodliffe, Oliver, Laker, Bulman,
Berquez, Maamria, Boyd, Stamp, Nurse (Weatherstone 80).
Subs Not Used: Gore, Quinn, Miller, Hocking.
Booked: Oliver, Nurse, Goodliffe, Stamp.
Goals: Stamp 38, Nurse 77.
Ref: S Tomlinson (Hampshire).