Trotters boss Sam Allardyce included Stelios Giannakopoulos in his starting line-up despite continuing transfer speculation, while Jared Borgetti was on the subs bench.
Graeme Souness welcomed back Shola Ameobi after injury, partnering the England Under-21 international with Alan Shearer in attack.
Shearer failed to beat the defensive wall with an early free-kick, before Stephen Carr had to be alert to deny Giannakopoulos a clear sight of goal at the other end.
However, neither keeper had been extended as the first half passed the midway point, although Bolton were forced to take off the injured Radhi Jaidi and introduce Abdoulaye Diagne-Faye for his debut.
The deadlock was finally broken eight minutes before the interval as Nicky Hunt crossed deep from the right flank and the unmarked El Hadji Diouf planted a free header past Shay Given in the Magpies goal.
Straight after the restart, Wanderers doubled the lead as Jay-Jay Okocha and Giannakopoulos made space for Hunt to cross and Diouf played the ball back from beyond the far post, Gary Speed headed on and Giannakopoulos was on cue to tap home.
Okocha drilled a 25-yarder narrowly wide of target as Bolton began to dominate, with the visitors replacing the ineffective Amdy Faye on the hour, bringing on Lee Clark.
Soon after Souness introduced James Milner in place of Lee Bowyer, but still Bolton kept the upper hand and Diouf almost added a third as he headed wide from a Giannakopoulos corner.
Shearer had a rare shot on target late on for Newcastle, but their hosts were in total control against a side lacking in ideas and confidence, with Borgetti given a debut right at the death.