Kevin McDonald's goal compounded Dunfermline's misery and kept Dundee in touch with league leaders Hamilton.
Derek Lyle almost gave Dundee the lead in the opening minute when he was inches away from Bob Davidson's cross.
Dunfermline came close to breaking the deadlock through Mark Burchill but his goalbound effort was cleared by Dundee's Eddie Malone.
McDonald struck 18 minutes from time when he collected Jani Sturm's pass and fired home from four yards.
Dunfermline: Gallacher, Woods, Murphy, Young (Williamson 84), Bamba, Harris, Simmons, Crawford (McGlinchey 46), Burchill, Hamilton, Glass. Subs Not Used: Scott Thomson, Scott Morrison, Murdoch.
Dundee: Samson, Worrell, Malone, McDonald, MacKenzie, Palenik, Robertson, McHale, Lyle (Zemlik 70), Davidson (Sturm 62), Swankie. Subs Not Used: Daquin, Dixon, Roy.
Goals: McDonald 72.
Ref: M Tumilty