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Until then Saints looked to have secured a precious away win after Gordon Strachan's tactics of fielding a largely defensive line-up and relying on breakaways seemed to have paid off.
After goalkeeper Antti Niemi had kept them in the game with crucial saves from Dean Holdsworth and Michael Ricketts, Wayne Bridge shot them ahead in the 82nd minute with a thundering left-foot shot.
In a largely sterile first half Bolton laboured in front of goal while Saints wasted their best openings with some off-target shooting.
Bolton's best efforts came in a two-minute spell just before half time when Gareth Farrelly and Holdsworth were both denied by good saves from Niemi who had earlier saved efforts from Djorkaeff and Ricketts.
Saints, hoping to improve on a dismal goal record that had seen them score only three times in seven games, looked livelier in midfield than the home side in the first half but failed to capitalise as Fabrice Fernandes, Rory Delap and Michael Svensson all missed the target from good shooting positions.
Bolton livened up their attacking play but still found the Saints defence difficult to penetrate after the break.
When Bolton did finally break through they found Finnish international Niemi in superb form in the Southampton goal as he kept out goalbound efforts from Holdsworth and Ricketts.
The deadlock was finally broken in the 82nd minute with Bridge the unlikely scorer.
As the Bolton defence concentrated on marking substitutes James Beattie and Brett Ormerod, Bridge stole into the penalty area, avoided Ivan Campo's tackle and hit a left-foot shot past Jussi Jaaskelainen .
Within two minutes Saints could have had another when Ormerod's chip landed on the roof of the net after the home defence had been caught off guard.
To their credit Bolton never gave up and they were rewarded two minutes into stoppage time when Djorkaeff finally beat the outstanding Niemi.
In contrast Bolton manager Sam Allardyce was relieved at the final whistle: "I'd have been dejected had we got nothing from the game," he said.
"It shows that good performances are important but the result is crucial."