The Pars are now two points clear of relegation rivals Livingston and will meet Motherwell again in the Cup final in March if the 'Well can upset Celtic in Wednesday's second semi-final.
Following a tame start Brian Kerr went close from long range and Scott McDonald had an overhead kick saved for the visitors.
Within seconds Dunfermline took the lead when midweek cup hero Darren Young drilled an angled right -foot effort low into the far corner.
The best move of the match then saw Noel Hunt back heel the ball for Simon Donnelly who forced a fabulous one-handed stop from keeper Colin Meldrum.
Motherwell lacked any cutting edge until shortly before half time when Richie Foran crashed a half volley against the post and the ever dangerous McDonald twice tested Allan McGregor.
McGregor made an even better save from Jim Hamilton's glancing header, but could do nothing about the tap in which gave Hamilton an equaliser early in the second half.
Mark Burchill replied with a fierce header which Meldrum parried, while McGregor continued his impressive display with a full length diving save to push away a 30-yarder from full-back Steven Hammell. Luck also came to Dunfermline's rescue when McDonald caught the bar with his left foot.
In a nerve racking last 10 minutes McGregor made another save from McDonald and home sub Stephen Simmons failed to make it a dream debut when he finished weakly with only Meldrum to beat.