A goal from Stevenage substitute Kyle Wooton just seconds after coming onto the pitch was enough to give the home side the points.
The home side had taken the lead in the 25th minute through Matt Godden.
The striker, who had gone close on two occasions early in the game, was played in behind the Morecambe defence down the left-hand side and he kept his cool to produce a fine finish to beat Barry Roche from a tight angle.
The Shrimps were level 10 minutes later with a well-worked set piece.
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Michael Rose swung in a pinpoint free-kick from the left-hand side and Steven Old nipped ahead of his marker to head past Joe Fryer from six yards for his first goal in Morecambe colours.
Jim Bentley's side went close to taking the lead on 41 minutes when Kevin Ellison raced onto another fine Rose cross but saw his effort go inches wide of the left-hand post.
The home side had the better of things after the break however and created a number of openings with Ronnie Henry firing wide from the right hand side when he should have done better, Godden also drawing a fine save from Roche before Wooton struck the decisive goal on 65 minutes with virtually his first touch of the game.
The big striker received the ball with his back to goal but turned smartly and struck his low shot past Roche.
Stevenage pressed for a third with Tom Pett seeing a shot cleared off the line by Aaron McGowan and Godden again denied by Roche before the Shrimps laid siege to the home goal with Fryer saving superbly from McGowan’s long range effort and a late Vadaine Oliver header that was heading for the top corner.
Despite the late pressure the Shrimps could not find the leveller and headed back north empty handed.
Stevenage: Fryer, Henry, Franks, Vancooten, Martin, Pett, Gorman, Smith, Kennedy, Godden (Samuel 84), Newton (Wooton 65). Subs not used: Day, Whelpdale, Beautyman, Conlan, Toner.
Morecambe: Roche, McGowan, Muller, Old, Brough, Kenyon (Lang 60), Wildig, Ellison, Rose, McGurk (Oliver 41), Thompson (Campbell 77). Subs not used: Nizic, Lund, Osborne, Lavelle.
Referee: John Busby.