Lawrie Sanchez's team dropped into the bottom three after Sunderland had picked up a point earlier in the day. But, after a game of little incident and few chances, it will be Sam Allardyce who will be feeling more comfortable heading into the Christmas period.
Newcastle were the better side and deserved their victory, achieved when referee Howard Webb ruled that Elliot Omozusi - on his 19th birthday - had fouled Alan Smith in the area.
Barton struck his penalty hard and low to Antti Niemi's left to give the north-east side all three points.
The first half was very much a war of attrition with Fulham in particular struggling to impress.
But against the run of play it was the hosts that nearly took the lead on 11 minutes when David Healy burst through on the right. Seeing Shay Given off his line, the Northern Ireland international opted for a cheeky chip which the keeper was forced to claw away for a corner.
Barton had the best chance of the half, climbing highest at the back post to meet James Milner's teasing cross. But, although the former Manchester City man got enough power into his header, it was too close to Niemi who clutched the ball at the second attempt.
Fulham were abject, although the boos and cries of 'you don't know what you're doing' as Sanchez reappeared for the second half were surely premature, considering that he has been in charge for only eight months.
And Sanchez's side improved, although central defender David Rozehnal should have put the visitors ahead on the hour. He managed only a slight touch to Charles N'Zogbia's free-kick when full contact would surely have brought the opening goal.
Rozehnal then missed an equally good chance with ten minutes to go, arriving late at the back post to meet another N'Zogbia set-piece, but he pulled the ball back too far in front of forward Mark Viduka.
The home fans were growing increasingly restless but their side looked short of ideas, despite Sanchez's decision to replace Steven Davis with Shefki Kuqi to give them more of an attacking thrust.
But with the game meandering to a forgettable draw, Smith went down in the box and Barton slotted home his first goal for the club to send the 5,000 Newcastle fans behind the goal delirious and increase the pressure on Sanchez.