The Trotters had come from two goals down to go in level at the interval but soon things where to go wrong as Jermaine Johnson was dismissed for an off the ball incident with Hugo Viana and then the Magpies hit a late winner courtesy of Bradley Orr.
Newcastle took the lead on five minutes through England U21 striker Shola Ameobi after he was able to take the ball from his own half to put the ball past the Bolton keeper Kevin Poole. A few minutes later the Magpies went further in front when Bolton debutant Bedi Buval turned the ball through his own goal in his first start for the reserves and one which he would rather forget.
Bolton where quick to respond as after a quarter of an hour they had pulled a goal back through the ever improving Mario Jardel who hit a stunning volley past Adam Bartlett in the Magpies goal after good work on the right hand side by Nicky Hunt.
Jardel had a couple more chances to convert, the first was saved well by Bartlett in the Newcastle goal and the second chance was inches over the bar following a good run by Jeff Smith.
On 39 minutes the Wanderers where level again, Jardel added his second goal of the night beating a couple of defenders following a good pass from Derek Niven before firing a superb right foot shot past the stranded Bartlett.
Ameobi could of put the away side further in front after he was found unmarked in the box but the veteran goalkeeper Poole stood equal to the shot from the 21-year old.
Shortly before the break the Wanderers could of gone into the lead, Jermaine Johnson decided to go alone and shoot over the bar but he had a number of other options available to him.
However the second half was to mark a change in fortune for Bolton, despite having lots of possession they just couldn't find the third goal to claim the points and this wasn't helped by the dismissal of Johnson who was sent off early in the second half for throwing a punch at Viana.
Orr hit the winner for the Toon Army on 51 minutes with a strike which would be suited to win any game, intercepting a pass from Darren Ambrose before unleashing an excellent 30-yard strike beyond the reach of the Wanderers keeper Kevin Poole.
BOLTON RESERVES: Kevin Poole, Nicky Hunt, Jeff Smith, Bedi Buval, Charlie Comyn-Platt, Glenn Little, Per Frandsen, Derek Niven, Jermaine Johnson, Mario Jardel and Jonathan Walters.
SUBS NOT USED: Jeremy Bon, Nidiwa Lord Kangana, Cleveland Taylor, Lewis Hamlin, Ricardo Vaz Te
NEWCASTLE RESERVES: Adam Bartlett, Kris Gate, Robbie Elliott, Steven Taylor, Gary Caldwell, Bradley Orr, Martin Brittain, Hugo Viana, Michael Chopra, Shola Ameobi and Darren Ambrose (Andrew Ferrell)
SUBS NOT USED: Lewis Guy, Smith, Carr, Peter Ramage