Lewis Sturman had forced home a 40th minute equaliser from a Keiron Elliott corner, but United conceded again before half-time as City netted what ultimately proved to be the winner.
United named a strong XI for the third round encounter but were unable to overcome a resolute Birmingham rearguard, with Charley Sanders rattling the crossbar with 11 minutes to play.
Boston (3-5-2): Sam Vince; Charlie Melville, Niall Delahoy, Lewis Sturman; Aaron Eyett, James Reed, Keiron Elliott, Jordan Sowerby (Leon Squire 66), George Stainfield; Charley Sanders, Jordan Nuttell. Subs (not used): Lewis McKue, Juris Kormis, Karolis Andriulionis.