Chester's 18-game unbeaten run was brought to an abrupt end as Stevenage ran out deserved winners at the Deva Stadium.
The Conference leaders were for the large part second best as a positive performance by the visitors condemned them to a shock defeat.
Chester had enjoyed the early possession and on five minutes Daryl Clare tested Lionel Perez with a curling shot that the keeper gathered at full stretch.
Two minutes later the visitors responded and were left ruing their luck as a 20-yard effort by Rocky Baptiste struck the bar with keeper Wayne Brown stranded.
Stevenage looked like they had every intention of going for a win and Gary Holloway and Anthony Elding both went close with shots on the Chester goal.
The home side should have taken the lead on 27 minutes as Kevin Rapley got on the end of Scott Guyett's cross, but the striker somehow managed to send his header from only six yards out past the post.
Keeper Perez managed to keep his side on level terms with a point-blank save to deny Guyett, who looked odds on to score.
Boro then shocked the Conference leaders with a goal eight minutes before the interval as Dino Maamria got to the byline and flashed the ball across the face of goal for Elding to head in from close range.
The response from Chester saw Clare a whisker away as his curling effort on the hour mark went a foot past the post, and 13 minutes later it was tough luck on Chester as a Ben Davies free-kick hit the upright.
With Chester still shaking their heads after their near miss the visitors promptly broke away and doubled their lead with Baptiste slotting home from Maamria's lay-off.
A Michael Twiss goal two minutes into added time gave Chester hope, but it proved too little too late.