It was a quiet return for Christie who missed several chances in the first half, but a welcome return for the forgotten forward.
Boro took the lead through an Adam Johnson free-kick but Bolton hit back through Matt Jansen and then Boro gifted them the lead just before half-time, as Brad Jones fumbled and the ball richoceted off Colin Cooper and into the net.
As Boro pushed for an equaliser they conceded another OG as John Johnson clipped a cross past Jones.
So Bolton inflicted Boro's first home defeat of the season in their final outing, and ruled out the lingering and slim chances of Boro winning the Reserve League North.
Boro team:
Jones, J Johnson, Grounds, Walker, Bates, Cooper (Williams), Fisher (Thompson), Kennedy, Christie, Craddock, A Johnson