Newcastle have now scored first in every game at home this season but managed just one win.
Worryingly, the fans vented their anger with some force as the Newcastle players allowed their heads to drop after a resurgent Wanderers grabbed the points with two close-range goals from El Hadji Diouf in a two-minute spell just before the hour-mark.
Even then there was plenty of time for Newcastle to bounce back but that never looked like happening.
Newcastle started off brightly with some slick passing that posed plenty of problems for Bolton with Emre heavily involved.
A surging Peter Ramage run down the left created the first opening with Obafemi Martins ducking under the cross which was bundled over the bar by Shola Ameobi without the striker ever being in control of the situation.
The deadlock was broken after 19 minutes from the penalty spot after linesman Glenn Turner spotted Abdoulaye Faye handle Stephen Carr's cross.
The ball certainly struck Faye's right arm and all protests were brushed aside.
Ameobi coolly slotted the ball to Jussi Jaaskelainen's right to make it three goals conceded by Wanderers this season from the penalty spot out of a total of just four against.
Steve Harper had nothing to do until the 35th minute when he made three rapid saves.
First he clawed out from skipper Scott Parker who slid in to rob Nicolas Anelka. The ball dropped for Kevin Nolan and Harper beat the ball away and recovered to push the rebound away from Anelka.
United should then have gone 2-0 up on the stroke of the interval. Damien Duff's left-wing cross was headed across goal at the back post by Ameobi, touched on by Martins for Ramage who, with the goal at his mercy, lifted his effort over the bar from seven yards.
That was the let off that Bolton needed as they were transformed in the second half - but not until after an early scare.
That came when Martins' pace took him clear and Jaaskelainen made a great parry as the striker shot across him.
The warning signs were there seconds later when Ramage was required to make a last-gasp challenge to prevent a Nolan equaliser.
But those alarm bells were not heeded and Diouf pounced after 55 and 57 minutes to seal the three points.
A raking long pass across the park found Carr napping. Anelka then won possession and crossed for Diouf who lost Titus Bramble and enjoyed a simple tap in.
Needlessly Diouf taunted the home fans with his celebrations, something he did again less than two minutes later when Bramble was once again caught wanting and Diouf was left with a simple close-range header.
Newcastle were totally shot and devoid of ideas and the jeers at the final whistle told Glenn Roeder what was thought of his team's display.