Carr, who was coaxed out of retirement by McLeish two seasons ago, suffered the setback in training ahead of the new campaign.
But he has played in the opening two league games and will return at Bolton on Sunday after being rested for the midweek Carling Cup tie with Rochdale.
McLeish said: "Stephen has been playing with a broken toe and been having injections to help him get through the games so far.
"I can tell you that is not nice but it also shows the type of character that he is.
"The good thing is he will get a decent rest after tomorrow's game because of the two-week international break and that should benefit him."
Carr's determination to continue playing has been crucial for Blues as their other senior right-back, Stuart Parnaby, has been suffering with a hamstring injury.
The former Tottenham and Newcastle player hung up his boots in 2008 but McLeish persuaded him to sign for Birmingham and he has been a key performer.