Queen of the South set up a Challenge Cup quarter final tie at home to Morton thanks to a fine win at East End Park.
The visitors took the lead after three minutes when Stewart Kean controlled a cross from Steven Tosh and unleashed a powerful shot past Callum Reidford.
Dunfermline went close when Nick Phinn's header was tipped on to the crossbar by Cameron Bell.
Queens doubled their advantage on 75 minutes when a Paul Burns cross was headed home by sub Sean O'Connor.
Dunfermline Ath: Reidford (Gallacher 44), Shields (Dearden 46), Muirhead, Phinn (McCann 61), Scott Thomson, Bamba, Willis, Ryan Thomson, Williamson, Kirk, McBride. Subs Not Used: Whyte, McGregor.
Queen of the South: Bell, Reid, Harris, Adams, Barr, Thomson, Arbuckle (McQuilken 44), Tosh (MacFarlane 84), Kean, Dobbie (O'Connor 60), Burns. Subs Not Used: Robertson, Halliwell.
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