It was Birmingham's first away victory in seven games since Boxing Day and Doncaster's first home defeat in nine matches.
Rovers had as much of the play as their opponents but could not find a way past the impressive City defence, although Matt Mills was unlucky to see a goalbound header cleared off the line.
Doncaster were on top at the start and it needed a full-length save from Maik Taylor to prevent them taking the lead in the seventh minute.
City gave away a free-kick just outside the box and Martin Woods had a well-struck low shot saved by Taylor, who did well to tip the ball round the post.
Birmingham looked determined to give nothing away playing with five men in midfield, leaving Cameron Jerome to go it alone and attack.
But the City striker proved a handful for the home defence and gave his side the lead with a superbly placed header in the 19th minute after latching on to a right-wing cross from Sebastian Larsson.
The goal came against the run of play but Birmingham almost scored again in the 32nd minute when Jerome hit a fierce shot just wide from a difficult angle after Sam Hird had presented him with the ball.
Another Doncaster gift handed City their second goal in the 42nd minute when Hameur Bouazza seized on a weak back pass from James Chambers to slot the ball past stranded keeper Neil Sullivan.
Rovers made a couple of substitutions at the start of the second half and James Hayter had a shot tipped round the post in the 50th minute before Mark Wilson saw a cracking 20-yard volley well saved three minutes later.
Birmingham defended superbly under pressure and broke out to almost score again when Stephen Carr had a shot cleared off the line following good work by Lee Bowyer in the 62nd minute.
Mills was denied by Carr's goalline clearance with Taylor beaten and Rovers were out of luck again when a free--kick from Woods was scrambled to safety two minutes from time.