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The home side's best chance to equalise came in the 43rd minute when Gray unleashed a screamer from the edge of the box, which Bolton goalkeeper Andy Lonergan met with a fingertip save to maintain his side's advantage at the break.
The second half was a scrappy affair as rainfall made for a greasy playing surface, and it as Birmingham who adapted better, almost drawing level through another Gray effort in the 70th minute which Lonergan to be alert at his near post.
Lonergan was the busier of the two goalkeepers, but it was his opposite number, Darren Randolph, who stole the headlines for the wrong reasons when he received a red card for bringing down Craig Davies in the area.
With striker Lee Novak in the Blues goal, Bolton should have made it two from the spot, but were made to settle for a 1-0 Championship win in the end as Davies put his penalty into the stands.