Scorers: Grant (67)
A spectacular Matty Grant effort from distance gave Stranraer three vital points to extend the gap at the bottom of the table.
The Blues were looking for back-to-back wins at Stair Park after defeating Spartans earlier this month.
They were also looking to bounce back from defeat last time out against Clyde.
Manager Chris Aitken made three changes from the loss at New Douglas Park as Finn Ecrepont, Aaron Quigg and Grant replaced Tomas Brindley, Mark Russell and Robbie Foster in the starting line-up.
Elgin started the brighter as they looked to build on a season which has them looking like genuine play-off contenders.
They had the first real chance of the afternoon when a ball over the top caught out the home defence.
Kane Hester rounded goalkeeper Josh Lane, who managed to prevent the frontman from getting an early shot away.

When he did pull the trigger, he found his route to goal blocked by Lewis Reid.
Stranraer came more into the half as it progressed and Ryan Edgar called Thomas McHale into action.
The striker weaved his way past two defenders but his fierce drive was deflected round the post.
The second half started in much the same fashion, with the long-travelled visitors doing much of the attacking.
Their best two chances came around the hour mark and on both occasions Stranraer had Lane to thank for keeping the scores blank.
First, Elgin capitalised on hesitation in the Stranraer box to seize possession and then cross in for Jack MacIver.
His effort seemed to destined for the top corner but Lane did brilliantly to push it round the post for a corner.
Then, a ball in from the left was met by Russell Dingwall, with Lane again pushing the ball over the crossbar.

Stranraer would find the game’s only goal and it came in memorable fashion.
It would be fair to say there seemed little danger when Grant collected the ball in front of the home dugout but his swirling lob outfoxed McHale and dropped beneath the crossbar.
Whether the shot was intended, only Grant will know but it proved to be the match-winner.
Understandably, the visitors pushed for a leveller but Stranraer’s defence looked reasonably firm over the remaining 20 minutes or so.
Hester blasted over the bar before Elgin made a treble substitution to try to get back into the game.
Their final chance would come as the game entered stoppage time.
The ball was swept back to the edge of the box where Mark Gallagher was waiting but his strike lacked the necessary power to overly test Lane.
Three welcome points for Stranraer, who will be looking to make it back-to-back wins in the league when Stirling Albion visit next weekend.
Stranraer: Lane, Ecrepont, Reid, Ross, Docherty, Robertson, Dunlop (Lang 87), Quigg, G Gallagher (McKnight 38), Grant (Guthrie 87), Edgar (Foster 78).
Not used: Brindley and Kane.
Elgin City: McHale, Booth, Dolzanski, Cameron (Draper 50), Girvan (Cairns 81), M Gallagher, MacIver, Hyde (Leslie 70), McDonald (Sargent 70), Dingwall, Hester (Golding 70).
Not used: MacDonald, MacEwan, Glavin and Taylor.
Referee: Colin Whyte
Attendance: 442
HT: 0-0
Photos: Bill McCandlish