Danish winger Bjarne Goldbaek's deflected second-half free-kick settled an entertaining encounter at Fratton Park.
Goldbaek, a £650,000 signing from Chelsea earlier this season, struck a 25-yard free-kick goal in the 73rd minute.
His shot took a wicked deflection off the Portsmouth wall and left on-loan goal keeper Russell Hoult stranded on the left-hand side of his goal - much to the delight of the Fulham fans gathered behind the goal.
Portsmouth, seeking their third successive victory under new manager Tony Pulis, had their chances before Goldbaek's decisive strike but in-form striker Steve Claridge had a second half goal disallowed while he also hit a post and strike partner Lee Bradbury blasted wide with only goalkeeper Maik Taylor to beat.
Portsmouth fielded the same team for the third match in a row as they looked to build on morale-boosting victories against Barnsley and Huddersfield but it was Fulham who created the best chances of the first half.
Striker Geoff Horsfield was only inches away from converting Goldbaek's cross into the six-yard area in the seventh minute and Goldbaek was again the provider on 32 minutes as defender Andy Melville wasted the best chance of the opening period.
Melville rose above the Portsmouth defence at the near post but could only send his header wide from eight yards out.
But Portsmouth came back strongly in the second half and should have taken the lead in the 49th minute through Bradbury. The former Crystal Palace striker raced on to Kevin Ball's under-hit back pass and only had Taylor to beat but he inexplicably dragged his shot wide of the left-hand upright.
Claridge had the ball in the back of the net on 58 minutes when he headed home Michael Panopoulos' corner kick but the effort was disallowed after the ball was adjudged to have gone out of play.
Goldbaek's strike was the signal for Portsmouth to surge forward in search of an equaliser but Claridge was again guilty of missing a great chance in the 81st minute.