The visitors had the first sniff of goal of the game 13 minutes in when Jacques Maghoma scuffed his effort wide for a goal kick after cutting in from the left-hand side.
At the other end, Will Buckley had a chance but sent his header wide of the far post as efforts remained at a premium for most of the first half.
Birmingham took the lead with just four minutes left of the opening period when Lukas Jutkiewicz applied the finishing touch to Maghoma's inswinging free kick to rifle into the roof of the net.
Despite their numerical disadvantage, however, Blues goalkeeper David Stockdale was seldom troubled and the West Midlanders held on for all three points.
BOLTON WANDERERS (4-3-3): Alnwick; Taylor, Beevers, Flanagan, Burke; Osede (Noone 56'), Vela, Henry (Kirchhoff 75'); Buckley (Clough 72'), Ameobi, Le Fondre
BIRMINGHAM CITY (4-4-2): Stockdale; Harding, Morrison, Dean, Colin; Jota (Kieftenbeld 77'), Ndoye, Davis, Maghoma (Dacres-Cogley 84'); Adams, Jutkiewicz (Roberts 90')