In a dramatic finale Stevenage snatched all three points with the winner coming deep into injury time.
And after 66 minutes of hard-fought but dull football, it was the introduction of George Boyd for the home side which made the difference as the Stevenage substitute scored and made the winner to leave Carlisle stunned.
Such an ending hadn't looked likely as Carliisle, buoyed by their opener on 20 minutes, had the measure of Stevenage.
With few chances created it was Peter Murphy who put Carlisle ahead, his free-kick from 30 yards out curling high into the top corner after home keeper Alan Julian had left the ball expecting a defender to get in a clearing header.
Stevenage looked for a way back into the game with Dino Maamria seeing a close-range effort blocked by Carlisle keeper Kieran Westwood while the home fans thought they had a good shout for a penalty when Darryn Stamp appeared to be pushed in the area.
The second half began in similar fashion with Stevenage looking unlikely to make the breakthrough until the introduction of Boyd with 25 minutes to go.
The tempo of the game then changed with Carlisle firmly on the back foot, and although Karl Hawley had two good chances to clinch it for the visitors, it was Stevenage who were destined to take the points.
Boyd drove home through a pack of players on 85 minutes before a siege on the Carlisle goal was ended when Jon Brady drilled high into the roof of the net in added time after a Boyd cross in from the left was only parried by Westwood.