The Frenchman, whose brace sank Manchester City last Saturday, scored Bolton's second goal after the visitors took an early lead.
Anelka now has six for the season and is finally showing the form that persuaded Sam Allardyce to part with £8million in the summer.
His 57th minute tap in makes him the club's leading scorer and gave Allardyce's team a Premiership double over the Geordies.
It was also the Lancastrians fourth successive league win to keep them challenging for a Champions League place.
However, it needed an unnecessary own goal to allow Bolton back into the contest after Kieron Dyer had fired the visitors in front.
Dyer made the most of some poor defending from their hosts, seizing on a weak chest pass by Kevin Davies, holding off the challenge of Tal Ben Haim and shooting underneath Jussi Jaaskelainen.
It could have been 2-0 after 17 minutes when Abdoulaye Faye mis-kicked allowing Obafemi Martins a clear sight of goal. Fortunately for Wanderers, the Nigerian screwed his left-foot effort wide of the target.
Jaaskelainen then tipped away a James Milner free-kick as Newcastle kept up the pressure.
But two minutes later all the good work of the first hour was undone. Former Newcastle hero Gary Speed headed into the United penalty area and Peter Ramage, under pressure from Kevin Nolan, headed past Pavel Srnicek.
Newcastle later claimed Nolan had shoved Ramage to make him lose control but there were few protests at the time.
And with such an inexperienced back four playing together for the first time in front of a hesitant Srnicek, there was always scope for errors.
From that moment, Bolton took control and Speed volleyed over from Anelka's cross.
Kevin Davies was booked before the break by referee Howard Webb, while Nicky Butt and El Hadji Diouf also picked up cautions during a flurry of yellow card.
Bolton made it 2-1 when Ivan Campo's long throw was flicked on by Davies. Diouf swung out a left leg diverting the ball to the far post where Anelka slid in.
Campo, Giuseppe Rossi and Paul Huntington went into Mr Webb's notebook as tempers frayed.
Bolton clearly thought they had the match won but their show boating passing routine didn't win them any plaudits from an angry Allardyce.
Newcastle sensed a reprieve. Emre, on for the injured Dyer, tried his luck from distance while Jaaskelainen tipped away a 20-yard shot by Parker.
However, Wanderers held on without too many more scares to make it a happy Christmas for everyone at the Reebok.