McCann (59) had been lucky not to concede a penalty for handball just moments before he stabbed home from close range at The Riverside.
The result, which had seemed unlikely as Boro ran the visitors ragged in the opening 10 minutes, was enough to lift the Trotters out of the bottom three.
David Wheater, Stewart Downing and Tuncay Sanli all spurned good chances early on for the home side.
And when a Downing cross was deflected onto McCann’s arm, Boro thought they should have had a penalty, but the protests were waved away.
But Bolton hung in there and when the ball broke loose from Gary Cahill’s header, Ross Turnbull failed to gather and McCann pounced from close range.