Hosts Newcastle created the better of the chances during the opening 45 minutes, but they were unable to beat Mark Schwarzer in the Fulham net.
Cisse and Yohan Cabaye had the better openings, but neither made the most of their opportunities from inside the penalty area.
© PA Photos
The Magpies continued to dominate proceedings after the restart and hit the woodwork on three separate occasions.
First Vurnon Anita struck the bar with a deflected drive from distance in the 53rd minute. Then with 63 minutes played, Yoan Gouffran headed against the crossbar, before Cisse turned the rebound against the upright.
However, just when it looked as though they were going to have to settle for a draw, Newcastle claimed a late winner. Fulham failed to clear their lines and Cisse was on hand to poke in from close range.