However, as former Newcastle striker Mitrovic hit the spot kick and hit it against his standing leg before the ball found the net, the goal was disallowed as he had touched the ball twice.
It looked as though Newcastle would have to settle for a third successive Premier League goalless draw before Isak arrived just before to slot home an 89th-minute winner, sparking wild scenes of celebration across the north east.
The win ensured Newcastle moved back into third place behind Manchester United in the standings on goal difference, one point behind champions Manchester City in second place. Fulham finished in sixth place.
Newcastle have 38 points from 19 games – their most at the halfway mark of a season in the competition since 2001-02 (39), when they finished fourth.