Jim McIntyre proved a wise inclusion for Ian McCall
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Jim McIntyre returned to the Dundee United side to score the deciding goal as Dunfermline suffered a blow to their European qualification hopes.
The Pars created the better chances but lacked the guile up front usually provided by the absent Craig Brewster.
McIntyre grabbed the winner with an excellent quick turn and shot into the far corner of the net after 57 minutes.
Victory stretched United's run to five home games without defeat and prevented the Pars leapfrogging third-top Hearts.
United manager Ian McCall had dropped captain Derek McInnes to the bench and drafted in Chris Innes, out for two months with a groin strain.
Andy McLaren was also left out, his place up front being taken by McIntyre.
Dunfermline boss Jimmy Calderwood made two changes, Aaron Labonte deputising for injured veteran striker Brewster and Greg Shields replacing Gary Dempsey.
An Andrius Skerla header following a corner was cleared off the United line by Alan Archibald as the visitors started brightly.
Stevie Crawford turned marker David McCracken and unleashed a powerful low drive from the edge of the box that Paul Gallacher did superbly to turn wide at full stretch.
Shields (left) was making his first start back with the Pars
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United produced some pressure of their own, McIntyre connecting with a Billy Dodds cross to the back post only for his header to be blocked for a corner off the body of Scott Wilson.
Dunfermline missed a great opportunity when Crawford got to the by-line and his cross found Thomson, but the Pars captain steered his header wide from 10 yards.
The Pars paid for those misses 12 minutes into the second half, when McIntyre drove the ball low into the far corner of the net after being set up by Charlie Miller.
Dunfermline ought to have equalised when a clever Thomson free-kick found Crawford in acres of space in the box, but the Scotland strike struck his half volley into the side-netting.
McIntyre came close again with a lobbed shot that nestled on the roof of the net.
Darren Young fired in a thundering volley that cleared the United crossbar by a matter of inches.
Dundee Utd: Gallacher, Wilson, Innes, McCracken, Archibald, Kerr, Miller, McIntyre (Easton 90), Robson, Dodds, McLaren (McInnes 62).
Subs Not Used: Bullock, Duff, Scotland.
Booked: Innes.
Goal: McIntyre 57.
Dunfermline: Stillie, Shields, Scott Wilson, Skerla, Scott Thomson, Darren Young, Nicholson (Dempsey 84), Mason (Hunt 68), Labonte (Tod 46), Crawford, Derek Young.
Subs Not Used: Ruitenbeek, Byrne.
Booked: Derek Young.
Attendance: 5,564
Referee: K Clark