Pardew missed the clash as he began serving his sanction for his headbutt on Hull City's David Meyler, having been given a three-game stadium suspension and four-game touchline ban by the FA.
Assistant manager John Carver took charge in Pardew's stead, but he could not inspire the visitors to a third consecutive win.
And Pardew, reportedly watching the action from a hotel suite in London, will have been largely unimpressed with his side's display as bottom club Fulham produced a dominant second-half display to take the points.
It was a mistake from one of Newcastle's more dependable servants that proved to be the difference, goalkeeper Tim Krul allowing a seemingly harmless long-range effort from Ashkan Dejagah to creep into the bottom corner to hand Fulham boss Felix Magath his first win since taking over last month.
Krul was the first of the two goalkeepers to be called into action just after the half-hour mark, the Dutchman diving to his right to keep out Lewis Holtby's effort from the edge of the area.
The visitors gradually grew into the game and would have taken the lead before the break had David Stockdale not produced a fine reaction save to prevent Cisse from turning home Moussa Sissoko's right-wing cross.
Fulham did have the ball in the net almost immediately after the break, but Pajtim Kasami's strike was ruled out after John Heitinga was ruled to have strayed offside before heading the ball back for the Swiss winger.
Newcastle then crafted a good opportunity at the other end but Luuk de Jong could only shoot tamely wide after latching on to Yoan Gouffran's pass.
Magath's men quickly began to dictate play and Pardew will have been thankful as the offside flag denied Fulham's teenage striker Cauley Woodrow.
Woodrow looked to have netted his first goal for the club when he prodded home a rebound after Heitinga's rasping drive had crashed off the underside of the crossbar and out, only for the linesman to rule out the effort.
Newcastle pressed in the final stages to try and find a leveller and were denied a penalty at the end.
Referee Howard Webb refused to point to the spot when Heitinga appeared to handle from Krul’s effort after the goalkeeper had come up for a late corner, ensuring that Fulham held on - although the London club remain four points adrift of safety.
