Dunfermline’s hopes of claiming a half-time advantage in this play-off were dashed by former East End star Stevie Bell.
The Pars looked to be heading for a draw when Faissal El Bahktaoui cancelled out Martin Grehan’s opener before the break.
But Jonathan Page was sent off for a second booking offence and Stranraer made the extra man count when Bell cashed in with a late winner.
Dunfermline boss Jim Jefferies declared: “Stranraer were up for it and won everything in the first 20 minutes.
“Some schoolboy defending cost us the early goal, which was really disappointing, but after that we dominated and played some good football.
“We should probably have made more of our chances, which is another disappointing thing.”
The home side started brightly and were in front after just 12 minutes through Martin Grehan.
Jamie Longworth showed fine control to take down a long punt from David Mitchell before being hauled down by Callum Morris as he dashed into the box.
The ball spilled to Grehan, who made no mistake from close range.
As the home side continued to assert authority, Sean Winter had a good chance to double the lead on the half hour mark but the midfielder pulled his volley wide of the post.
At the other end, Ross Millen scooped a free-kick over the bar from a dangerous position on the edge of the box.
However, the Pars were growing in strength and drew level four minutes before the break when Josh Falkingham set up El Bakhtaoui. The Frenchman provided a cool finish past an unprotected Mitchell.
Early in the second half, Stranraer had a great chance to edge in front again, as they attacked at pace, Page making a robust block to deny Winter.
As the Blues swept forward, Mark Docherty had a penalty claim denied as Ross Forbes robbed him just inside the box.
Dunfermline battled back into the game and El Bakhtaoui found space on the six-yard line, but sliced his shot wide of the goal.
Midway through the second half,Mitchell in the home goal stood up well to block Stephen Husband’s drive, after the substitute had been on the pitch less than a minute.
Moments later, Docherty made a last-ditch block after El Bakhtaoui’s shot from the edge of the box looked to have beaten the Stranraer goalkeeper.
With Dunfermline in the ascendancy going into the final quarter of an hour, Stranraer’s forays into the Dunfermline half were largely restricted to counter attacks, with Grant Gallagher having a strong chance to grab a winner after a dangerous break involving Longworth and substitute David McKenna.
In the closing stages, Stranraer again drove forward and Page was red-carded after a second booking in quick succession for a cynical trip on Longworth. Ryan Scully made a good stop from Andy Stirling’s resulting free-kick.
The home side weren’t to be denied a winner, however, with Bell doing the damage against his old side as he pounced at point-blank range to convert Andy Stirling’s free-kick two minutes from the end.
Despite the loss, Jefferies said: “It’s only half-time and the good thing is there’s not just 45 minutes to go but 90.”
Blues boss Stevie Aitken said: “We’re delighted with the win but we know there is still a long way to go. I thought it was a magnificent advert for Scottish football and my players were terrific.”