The Bolton Wanderers striker silenced the boo boys as he scored two first-half goals which heaped more pressure on City, whose worrying slide down the Premiership table continued following back-to-back home defeats.
Anelka who failed to find the net in his first eight Premiership matches for Bolton, has now found the scoring groove with five in the league and six in total for the campaign.
Micah Richards and Claudio Reyna were ruled out by injury, while Georgios Samaras was relegated to the substitutes bench for City.
Manager Stuart Pearce brought Nedum Onuoha into defence and Stephen Ireland and Ishmael Miller into midfield, enabling Darius Vassell to switch inside from the flank to partner Paul Dickov up front.
Bolton were without the suspended Kevin Davies and the injured Stelios Giannakopoulos as Tal Ben Haim and El Hadji Diouf returned to the starting line-up.
Anelka took only eight minutes to break the deadlock with an excellent finish to a neat passing move which he had begun.
Nicky Hunt provided the final pass and Anelka found the net with a clinical finish low inside the near post of keeper Nick Weaver.
City were unlucky not to be on level terms moments later when Bolton keeper Jussi Jaaskelainen made a brilliant save to keep out Dickov's close-range header, with the Scot claiming the ball had crossed the goal-line.
And not long after City had a penalty appeal rejected after Onuoha's shot appeared to strike the hand of Henrik Pedersen.
Bolton doubled their advantage against sorry City midway through the opening period with an effort he could not miss.
Pedersen played the ball in low from the left and it eluded the entire City defence, leaving Anelka completely free at the far post to pick his spot low to the left of Weaver.
And City left the field at half-time to what is becoming an all-too-familiar chorus of jeers from their disgruntled fans.
Jaaskelainen denied City for a second time early in the second half with an athletic save low to his left to turn away Joey Barton's free-kick.
Pearce made a double substitution ten minutes after the re-start as Ben Thatcher and Dickov were replaced by Samaras and Ousmane Dabo as City switched to a 3-5-2 formation.
City were denied a second penalty shortly before the hour when television replays revealed Abdoulaye Meite failed to win the ball and clearly fouled Vassell from behind.
Despite Pearce's tactical re-jig, City were unable to gain a foothold back in the game in the final half-hour as Bolton defended resolutely to hold on to their lead.
And City's troubles increased in the dying minutes when Barton was sent off following a crude lunge at Abdoulaye Faye.
Though contact was not made, referee Mike Riley produced a straight red card so Barton will now miss City's remaining three games of the holiday period.