The long-serving Jamaica international, 30, replaced the injured Mustapha Riga shortly before half-time and applied the finishing touch to a wicked low cross from Gretar Steinsson in the 77th minute.
It was the Trotters' first goal for five hours and 50 minutes and Gardner then turned provider by crossing for City skipper Richard Dunne to put through his own goal with two minutes remaining.
Megson said: "Bibi (Gardner) is one of the nicest people that you'll ever meet and the only reason he's not been in the side is that Matty Taylor's set-pieces are very good and he gives us a little bit more of a goal threat.
"Bibi came here and we put Matty on to the other side, and Bibi has scored the first goal and made the second.
"He wasn't out of the team through any other reason than we need to score goals but he's now come in and done that. I'm really pleased."