United had taken the lead through Dimitar Berbatov in a tight game of few chances at St Andrews before Bowyer struck in the 90th minute to earn his side a point.
"I think it is terribly harsh," said Ferguson, whose unbeaten side have won only one of eight away league games this season, having again relinquished two points late on as they did at Fulham and Everton early in the campaign.
"I think we outplayed them in the second half. We deserved to win the game, we were the better team.
"Maybe we should have finished them off. We just lacked a bit more care in our final pass and finishing."
United moved back to the top of the Premier League on goal difference ahead of Manchester City, and have two games in hand on their local rivals.
But they missed an opportunity to move five points clear of Arsenal - who visit Wigan on Wednesday - and nine clear of Chelsea, who host Bolton, from the same number of games played (18).
"At this moment there are five or six teams who are all contesting that area at the top but if you get to new year and you are in that front position then you have a great chance," added Ferguson.
McLeish pleased by home form
Birmingham boss Alex McLeish, whose side moved out of the bottom three courtesy of the point, had little sympathy with United.
"He [Bowyer] wasn't offside, definitely not," he said. "It does look as if it came off Zigic's arm, but I don't think he plays it deliberately off his arm.
"It would have been harsh if he had been penalized for deliberate handball."
He added: "I feel that we got our reward for perseverance, good concentration, tactical awareness. The players adhered to everything we asked them to do.
"United had a lot of possession but most of it was deep on the pitch which suited us.
"United cut us open at the start of the second half but we fought back well and got our reward.
"We are not at a safe distance away from the bottom of the table at present but these sort of points could be crucial, bonus points really."
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