The win gives caretaker manager Chris Coleman a win in his first game in charge, which also sees Newcastle once secure Champions League place - looking a little less certain.
Magpies captain Alan Shearer put his side ahead just before half time when he produced a typical header from a Hugo Viana cross.
The visitors were then reduced to ten men just after the hour mark when Andy Griffin was dismissed for two bookable offences.
Fulham took advantage of their larger numbers and levelled matters on 69 minutes when Sylvain Legwinski smashed home a wonderful drive from 30 yards.
Then with just minutes remaining, former Newcastle United hero Lee Clark was on hand to rifle home against his hometown club to give Fulham all three points and a much needed boost.
Fulham look all but safe from relegation now, whilst Newcastle remain in third, but fifth placed Newcastle are within three points of them.
