After the contentious decision to fire John Eustace, the 38-year-old was brought on board on October 11 with Blues sitting sixth in the standings.
Since then, they have dropped to 20th place; their 3-0 loss to Leeds on Monday was their ninth setback in his 15 games as manager.
"Football is a results business and I recognise they've not been at the level I wanted them to be," Rooney stated.
A member of Rooney's backroom staff, former Wales and Wolves footballer Carl Robinson, has also left Birmingham, and interim manager Steve Spooner will lead the team.
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