Jonathan Walters put the Premiership side ahead on 14 minutes with an unstoppable curling shot which beat debutant goalkeeper Clint Davies in the Town goal.
The visitors had chances to increase their lead with Walters being involved again but it was the home side who could have drawn level before half time when a clearance from the Trotters keeper Kevin Poole hit Andy Farrell but somehow the ball stayed out making sure the Whites went into the half time interval leading.
Farrell however did get onto the scoresheet on 64 minutes to make the scores level when he latched onto a ball fed to him by substitute Craig Midgley calmly slotting past Bolton's subtitute goalkeeper Ashley Timms who was on trial from Manchester City.
Timms made a good save from Farrell a few minutes later to stop the youngster from increasing the home side's lead.
On 75 minutes the home side hit the winner, Midgley was again involved and he picked out former Sheffield United midfielder Jon Cullen who fired an unstoppable volley past young keeper Timms in the Bolton goal.
Next up for the Wanderers is the tour of Malta next week but this experience should have given some of the younger members of the squad valuable experience against decent opposition.
BOLTON: Kevin Poole, Nicky Hunt, Jeff Smith, Danny Livesey, Charlie Platt, Ndiwa Lord-Kangana, Derek Niven, Gareth Farrelly, Delroy Facey, Jonathan Walters, Cleveland Taylor
SUBS USED: Ricky Shakes, Ashley Timms, Reece Jones, Jason Talbot, Reda Kribib
HALIFAX: Clint Davies, Darren Hockenhull, Kevin Sandwith, Steve Bushell, Mark Monington, Shaun Garnett, Ryan Mallon, Jon Cullen, Simon Parke, Andy Farrell, Sean McAuley
SUBS USED: Danny Hudson, Michael Senior, Craig Midgley