Kevin Doyle gave the home side the lead on 18 minutes when he headed home from Greg Halford's long throw.
They doubled their lead five minutes after half time when David Edwards smashed the ball home from Andy Keogh's clever pass.
Wolves looked to be cruising but Fulham halved the deficit on 66 minutes when referee Kevin Friend awarded the visitors a penalty for a pull on Bobby Zamora's shirt by Michael Mancienne - and Danny Murphy stepped up to slot the ball home.
Substitute Diomansy Kamara almost grabbed an unlikely equaliser for Fulham but his shot was cleared off the line by George Elokobi to ensure Wolves took all three points.
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