City led through Daphne Corboz's tap-in after Nikita Parris hit the post.
Steph Houghton's curling free-kick towards the bottom corner was well kept out by keeper Sophie Baggaley as the visitors dominated the game.
In second-half stoppage time, Jane Ross headed home Parris' pinpoint cross to secure all three points.
Birmingham's best chance came through Melissa Lawley whose drive was saved by Karen Bardsley, but the hosts were second best throughout.
Manchester City Women made it three wins from three to start the Women's Super League season with a hard-fought win at Birmingham City Ladies.