Newcastle are now in the top ten having been relegation candidates before Graeme Souness departed last month.
A second minute Emre corner should have posed bigger problems than it did. Gary Speed, who was making his 550th top-flight appearance, missed the cross to leave Jean-Alain Boumsong with a free header but he missed the ball.
Bolton, unbeaten in seven Premiership outings and with a top-five place up for grabs, went close with a Radhi Jaidi header and another from United old boy Speed.
Jay-Jay Okocha limped off after 17 minutes to be replaced by Hidetoshi
Nakata who could only watch as the woodwork came to Bolton's rescue seconds later to deny Emre.
Newcastle were then indebted to the woodwork as Bolton thought they had gone in front on the 24-minute mark. Nakata's deep cross was headed across goal by Speed and Kevin Nolan's first timer struck former Bolton defender Robbie Elliott, who knew absolutely nothing about it as it smashed against the upright.
Dangerman Nobby Solano pounced after 34 minutes for the third time in successive Saturdays at St James' Park with a stunning 25-yard free-kick.
Finnish keeper Jussi Jasskelainan could do nothing then, but was
Hopelessly at fault in time added on when he helped Alan Shearer's header into the net when he appeared to have it covered.
Newcastle increased their lead after 69 minutes. A corner was cleared as far as Celestine Babyaro whose volley went straight to Shola Ameobi who controlled the ball and picked his spot having being played onside by Ricardo Gardner who remained on the goal-line.
Bolton were offered a lifeline two minutes later when Gardner's back-post cross was headed across goal by Jaidi and Kevin Davies claimed the final touch.
Nolan was furious in the dying minutes when Bolton's leading scorer forced the ball into the net only for his effort to be ruled out for handball.