Scorers: Mason (12) and Healy (55)
Goals in either half gave Stranraer all three points on the trip to Ainslie Park.
The Blues remain top of League Two after Seb Mason’s first half header and a curling strike from Aaron Healy.
Chris Aitken’s side had drawn 3-3 with Kilmarnock B during the week and the manager made five changes from that line up.
In came Max Currie, Evan Dunne, Archie Traynor, Zach Bruce and Lewis Dobbie.
It was Stranraer who were first to threaten as Dobbie teed up strike partner Mason.
The frontman was heading away from goal but still managed to get his low shot on target, with Blair Carswell making the save.
The hosts, now under the management of James Craigen, had a couple of efforts from outside the box with Brogan Walls off target before Mark Stowe called Currie into action.
The opener would come after a series of throw ins on the left hand side.
Traynor hooked in a cross and Mason threw himself at the ball, glancing a header out of the reach of Carswell.
On-loan Kilmarnock man Traynor was denied by the goalkeeper as Stranraer pushed for a second but they had Currie to thank moments later.
Marc McNulty lifted the ball over the Stranraer defence for Ricardo Dinanga to run onto.
He got into the box and got a shot away, only for Currie to make the block with his right foot.
The goalkeeper again needed to be alert early in the second half as Spartans pushed for a leveller.
Stowe found a pocket of space on the edge of the box, turned and sent a shot towards the far corner.
Currie threw a hand up to push the ball into the air and then gathered the loose ball.
After those chances for the home side, Stranraer got their second goal.
Traynor played the ball out wide for Healy, who still had plenty to do.
The midfielder cut inside, escaped a challenge and then placed a shot beyond Carswell for his third goal in two league games.
Stranraer’s defence, who were once again impressive, saw the game out without too many more nervous moments.
The victory means Aitken’s side go into the Scottish Cup clash with Tayport top of League Two.
Spartans: Carswell, Whyte (Thomson 64), Tapping, Sonkur, Mudie, Welsh (Dall 78), Walls (Dishington 64), Heal, McNulty, Dinanga, Stowe.
Not used: McAllister, Ross, Taylor and Martin.
Stranraer: Currie, Coll (Gillie 82), Nair, McLuckie, Dunne, Quigg, Healy (Plank 72), Traynor (Dolan 72), Bruce (Stuart 65), Dobbie, Mason (Cleland 82).
Not used: Cameron, Foster and Henderson.
Referee: Grant Irvine
Attendance: 502
HT: 0-1