A sensational goal from the Frenchman and another strike for the red-hot Senegalese frontman keep the Toon well in the hunt for a top four finish
The win is the Magpies' fifth in a row in the Premier League, and sees them throw down the gauntlet to top four rivals Arsenal, Tottenham and Chelsea.
Bolton, meanwhile, remains 16th in the table, just one point clear of the relegation zone and with much work still to do in order to preserve its top-flight status for another season.
While the opening 70 minutes was battle of defensive wits, Ben Arfa quickly changed that in the 73rd minute.
The French midfielder's clever flick on the halfway line lost his marker and bought him the space to drive at the Bolton defense, carrying the ball the best part of 50 yards and majestically evading two more Trotters defenders before calmly poking the ball past a flailing Trotters keeper Adam Bogdan.
Then Cisse continued his siege on the Premier League.
Substitute Shola Ameobi impressively turned Ream and galloped down the right flank before delivering a pinpoint cross which Cisse gleefully tapped home for his 10th goal in nine matches.
Entering the match, both head coaches made some changes to their lineup. Toon boss Alan Pardew made one enforced change to the starting XI which beat Swansea on Friday, with Fabricio Coloccini returning in place of Cheikh Tiote, who failed to recover from an injury sustained at the Liberty Stadium.
Owen Coyle, meanwhile, made three changes to the Bolton side demolished by Fulham on Saturday, with Marcos Alonso, David Ngog and Ryo Miyaichi dropping to the bench and Gretar Steinsson, Chris Eagles and club captain Kevin Davies recalled.
An uninspired opening yielded no real chances for either side, as the visitors appeared content to establish themselves without committing too many men forward and the hosts lacked the penetration to build on numerous spells of fairly comfortable possession.
In these early moments it was defenders, rather than attackers, who caught the eye. Tim Ream recovered well to halt Cisse’s progress down the right flank, before Coloccini blocked Sam Ricketts’ shot from the edge of the area.
The Argentine then looked to contribute in attack, carrying the ball forward and lofting a precise ball in behind for the onrushing Demba Ba, but the Senegalese striker was denied a chance by a combination of his own first touch and the linesman’s flag.
Newcastle came closer to a breakthrough on 38 minutes, as Ben Arfa’s whipped free kick forced Bogdan to rush out in order to deal with the danger. The Hungarian’s punch, however, ricocheted dangerously off Ricketts and flew out of play.
Darren Pratley wasted a decent chance for Bolton on the stroke of half-time when he headed straight at Tim Krul from close range, but it was no great surprise when a first half which had offered nothing to merit a goal got the scoreline it deserved.
Coyle’s men began the second period with greater urgency and confidence, and Krul was forced into action in the 48th minute when Eagles jinked wonderfully away from two Toon defenders, only to be denied by the big Dutchman’s outstretched leg.
Newcastle looked rattled, and Bolton was left cursing their luck again moments later when Martin Petrov’s lashed cross from the left flank evaded Krul as well as Pratley and Kevin Davies by a matter of inches.
The visitors continued to carry the fight, and on 65 minutes Krul gathered gratefully after Mark Davies could only manage a scuffed effort from Kevin Davies’ dangerous looping cross from the right-hand side.
The Toon faithful raised the decibel level in a bid to wake their team from their slumber, and Ben Arfa came close to providing the desired response when he flashed a free-kick just wide with Bogdan scrambling for his post.
But the brilliant Frenchman was not to be denied, and with 73 minutes on the clock he produced what must be considered one of the goals of the season.
Coyle’s response was immediate, sending on Miyaichi, Ngog and Ivan Klasnic in a bid to give his side a route back into the game, but instead it was Newcastle who sealed the points seven points from time.
With a two-goal cushion, Pardew's men comfortably closed out another win which brings their Champions League dream one step closer to becoming a reality.