There was a run-out for ex-Bolton Bolton forward Michael Ricketts at the Reebok, while Bolton played ex-Boro keeper Kevin Poole.
The first half was dominated by the keepers, Ross Turnbull and Poole, who both made several good stops to keep the game goalless.
It was Boro who broke the deadlock after 65 minutes when Craig Dove scored from a narrow angle. Stewart Downing wrapped up the points in injury time with a powerful drive.
Boro team:
Turnbull
Cade
Wright
Close
Gulliver
Smith (Brunt)
Johnston
Wilson
Ricketts (Graham)
Dove
Downing