Despite a determined defensive performance from Fulham, the No.9's late strike handed the Magpies victory and eased their relegation fears as they pulled away from the drop-zone
The hosts bossed possession throughout but it seemed they would have to settle for a point before the Senegalese striker popped up in added time to send Newcastle six points clear of the drop-zone.
Alan Pardew made just one change to the side that were beaten in Portugal midweek with Yoan Gouffran replacing the injured James Perch but it was the visitors who started on the front foot as Dimitar Berbatov saw his curling effort sail just over Tim Krul’s crossbar.
An injury to Davide Santon forced the home side into an early change of personal as well as formation as Pardew reverted to his usual 4-2-3-1 formation with the introduction of Vurnon Anita. However, Fulham once again came close as Mapou Yanga-Mbiwa sliced his clearance from a Damien Duff cross and was fortunate to see the ball bounce out for a corner after he left Krul wrong-footed in the goalmouth.
Roared on by the passionate home fans, Newcastle began to control proceedings and put the Cottagers defence under increased pressure. Shortly after the half hour mark, the nippy Sylvain Marveaux played in Cisse on the left but the striker opted to shoot instead of returning the favour to the Frenchman who was in a better goalscoring position.
Moments later, Cisse linked with Gouffran to create the opening but when it seemed the substitute would slot past Mark Schwarzer from eight yards out, the linesman incorrectly raised his flag to deny the home side a glorious opportunity.
After failing to take advantage of gilt-edged chances at the other end, Newcastle were nearly made to pay just before the interval. After Berbatov led a Fulham breakaway, Krul pulled off a brilliant save to deny Stanislav Manolev after a goalmouth scramble from a corner.
The half-time break didn’t alter the flow of the game as Newcastle stepped up their pursuit of the breakthrough goal but were twice denied by the woodwork. Vernon Anita’s shot hit Emmanuel Frimpong's lazily outstretched leg, and with Schwarzer completely wrong-footed, the ball cannoned off the crossbar.
It seemed as if it was going to be one of those days for the home side as Marveaux's corner was headed goalwards by Gouffran but Riether’s outstretched arm deflected it onto the upright before Cisse smashed the rebound onto the same post.
The visitors offered little going forward in the second period but Berbatov thought he had scored with a free header from a John Arne Riise free-kick, only for Krul to acrobatically palm over.
The introduction of Shola Ameobi with a quarter of the game remaining added an extra dimension to the Magpies’ attack but as Fulham dropped deeper, the chances continued to be spurned.
However, deep into injury-time, Cisse turned the defence with a superb touch from a Yohan Cabaye shot and finished past Schwarzer to send the home fans into raptures.