Second-half goals from Scott Thomson and substitute Billy Mehmet gave Dunfermline a richly-deserved win.
The home side should have won by more but a combination of poor finishing and good goalkeeping from Paul Gallacher kept them at bay.
Dunfermline gave a debut to Australian midfielder Andy McDermott and brought back Andrius Skerla and Gary Mason as they sought to make amends for the CIS Cup defeat by St Johnstone in midweek.
The home side dominated the first half and United goalkeeper Gallacher had a busy time.
He clutched a lob from Barry Nicholson under his crossbar and then used his boot to deny Stevie Crawford in the early stages.
The goalkeeper had to leave his line swiftly to close down the angle as Gary Dempsey squeezed a shot narrowly wide.
But it was United who had the best chance of the first half after 25 minutes. Jim Paterson beat McDermott and Skerla on the left but his shot was too close to Derek Stillie and the goalkeeper manager to get a foot to the ball.
Dunfermline stepped up the pace towards half time and Craig Brewster sent a header just a yard too high before Nicholson tested Gallacher again with a head-flick which the goalkeeper dealt with comfortably.
Crawford missed a great chance at the start of the second half when he had only Gallacher to beat but sliced his shot wide of target.
The breakthrough came in 58 minutes when Dempsey's free-kick was headed past Gallacher by Thomson.
Crawford missed two more chances and Brewster another as Dunfermline pressed for the clinching goal.
But it did not come until a minute from time when substitutes Aaron Labonte and Mehmet combined for the latter to beat Gallacher from close range.