Luke Wilkinson’s injury-time goal saw Stevenage claim a dramatic three points at the Globe Arena.
In the fifth of eight added minutes, a corner ended with the substitute scoring from close range to spark wild celebrations from the visitors.
Kevin Ellison’s sixth goal of the season had earlier looked like helping Morecambe claim a share of the spoils after Ben Kennedy’s penalty put Stevenage ahead at half-time.
The Shrimps had made one change from the side which drew at Exeter City last weekend as Liam Mandeville came in for Alex Kenyon to play in the hole behind Ellison and Rhys Oates.
It meant a place on the bench for new loan arrival Richie Bennett, who was joined by youth team striker Freddie Price as injuries continued to hit the Shrimps hard.
Nevertheless, those absences could not be used as an excuse for a poor first half in which Morecambe were second best.
Stevenage were bright in possession, using the flanks to good effect, and their running off the ball continually posed problems.
Morecambe keeper Mark Halstead made two early saves from Moses Makasi and James Ball, while Danny Newton saw an effort deflected behind.
It was no surprise when they took a 25th minute lead as Steve Old half-cleared a cross and, in trying to claim the loose ball, could only trip Makasi.
It looked a clear penalty but referee Graham Salisbury took his time before pointing to the spot with Kennedy sending Halstead the wrong way from 12 yards.
Stevenage could have doubled that lead just past the half-hour when they broke at speed from a Morecambe corner but Makasi headed wide.
The Shrimps’ attacking play, in contrast, was laboured as they struggled to create anything in the way of genuine chances.
Andrew Tutte had a free-kick deflected behind and fired wildly off target from 25 yards and a brief flurry just before half-time saw Oates and Jordan Cranston shoot weakly at Paul Farman.
Eight uneventful minutes of the second half were all it took for Bennett to make his first appearance and he could have scored moments later.
Just after Cranston had almost shot out of the ground from 20 yards, his cross towards Ellison was diverted into Bennett’s path.
Seven yards out and one-on-one with the keeper, he could only blaze the ball wastefully over the bar.
Ellison curled an effort just off target before he dragged the Shrimps level with 20 minutes left, collecting Bennett’s lay-off to fire home..
He almost had a second four minutes later, cutting inside from the right, beating two men before seeing his shot comfortably held.
Morecambe thought they had a penalty when Zak Mills went to ground after Ellison’s shot was palmed out but the decision went against them.
Then, with time running out, a corner was headed in by Wilkinson to leave the Shrimps licking their wounds.
Morecambe: Halstead, Sutton, Lavelle, Old, Mills (McKay 90), Tutte, Cranston, Conlan, Mandeville (Bennett 53), Oates (Kenyon 85), Ellison. Subs: Szczepaniak, Brownsword, Hedley, Price.
Stevenage: Farman, Wildin, Nugent (Wilkinson 76), Cuthbert, Hunt, Kennedy (Reid 62), Timlin (Iontton 67), Byron, Makasi, Ball, Newton. Subs: Byrne, Sonupe, Henry, Smyth, Wilkinson.
Referee: Graham Salisbury.