Arsenal kept in touch with leaders Chelsea after a comfortable win.
Thierry Henry gave Arsenal an early lead with a calm finish after his trickery had bamboozled Ian Pearce.
For 15 minutes after the interval Fulham made a game of it as Tomasz Radzinski twice tested Manuel Aluminia and Collins John went close.
But after Henry had hit the woodwork, Pires' deft footwork and powerful shot made the game safe, a goal inspired by Dennis Bergkamp's clever dummy.
Fulham had ambitiously started with John and Radzinski partnering captain Andy Cole in attack.
But the visitors were never able to make full use of that attacking intent and all too often John and Radzinski were forced to drop into midfield as Arsenal assumed control for long periods.
Even so that brief period of Fulham ascendancy provided some nervy moments for Arsenal.
Papa Bouba Diop surged down the right and pulled the ball back, though he was let down by a lack of support for his teammates.
John and Radzinski also began to get into more dangerous attacking positions and Aluminia needed to come out quickly to gather the ball ahead of the former Everton striker.
Just past the hour John bustled his way past Gael Clichy, only to screw his shot wide of the post.
Radzinski also almost lobbed Aluminia, but the Arsenal keeper jumped well to save one-handed.
Francesc Fabregas and Patrick Vieira had much to do with Arsenal's periods of dominance and they were ably supported by Ljungberg and Pires on the flanks.
It was Ljungberg's pass to Henry that allowed the Frenchman to slip away into the penalty area, though he had still had to get past Pearce, who had tracked the Arsenal striker's run.
After feinting to shoot, Henry checked inside Pearce, leaving the Fulham defender on his backside, before curling the ball into the corner of the net.
Edwin Van der Sar had had to save a Pires shot just before Henry's goal and soon afterwards the Dutchman flung himself to his left to push away a Vieira effort.
Early in the second half Van der Sar made an even better save to deny Pires, who had burst clear, standing up until the last moment and deflecting the ball away with his feet.
But Pires was not to denied as he capitalised on some good approach play that saw Ljungberg cross and Bergkamp dummy, allowing the ball to run on to Pires.
Pires quickly dragged the ball on to his left foot before drilling it past Van der Sar.
Arsenal: Almunia, Lauren, Toure, Campbell, Clichy,
Ljungberg (Flamini 76), Fabregas, Vieira, Pires,
Bergkamp (Van Persie 78), Henry.
Subs Not Used: Lehmann, Senderos, Pennant.
Goals: Henry 12, Pires 71.
Fulham: Van der Sar, Volz, Pearce, Knight, Bocanegra,
Radzinski, Rehman (Malbranque 81), Diop, Pembridge, John,
Cole (McBride 66).
Subs Not Used: Legwinski, Crossley, Fontaine.
Booked: Rehman, Volz.
Ref: B Knight (Kent).