The visitors were left furious as it appeared that substitute striker Nicola Zigic had handled the ball in the build up to BowyerÃ¢â‚¬â„¢s 89th-minute equaliser.
United had earlier taken the lead through Dimitar BerbatovÃ¢â‚¬â„¢s 14th league goal of the season in the 57th minute.
The point sees United move back to the top of the Premier League table on goal difference, but they have now drawn seven of their eight away league games this season and will feel they have yet again dropped points on the road late on.
In a poor first half, in which neither team created any clear cut chances, Ryan Giggs came closest with a miss-hit cross that was tipped onto the post by former United goalkeeper Ben Foster.
BirminghamÃ¢â‚¬â„¢s best chance fell to Craig Gardner who blasted over from the edge of the area after good play from Bowyer and Sebastian Larsson down the right hand side.
The second half started in the same fashion as the first had ended, with both teams giving the ball away and not producing any rhythm in their attacking play.
United, however, showed their class to take the lead in the 57th minute through the league’s top scorer Berbatov.
The Bulgarian’s sublime backheel sent Darren GibsonÃ¢â‚¬â€a replacment for Ji Sung Park who is away on international duty with South KoreaÃ¢â‚¬â€running at the Birmingham goal and he fed Berbatov who expertly controlled the ball before slotting it past Foster on his near side.
A few minutes later Berbatov almost grabbed a second when he showed some quick feet on the edge of the area only to see his snap shot rebound off the post.
Apart from that moment of magic UnitedÃ¢â‚¬â€playing their second game in three daysÃ¢â‚¬â€looked sluggish and failed to reproduce the sparkling form they showed against Sunderland, while BirminghamÃ¢â‚¬â€playing their first match in 16 daysÃ¢â‚¬â€offered little real threat going forward, and it seemed that the visitors would leave St Andrews with three points.
But Birmingham manager Alex McLeishÃ¢â‚¬â„¢s decision to throw on 6ft 8in Zigic late on paid off as his physical presence unsettled the United defence, and he created BowyerÃ¢â‚¬â„¢s late equaliser to give the home side a vital point in their relegation fight.
United remain undefeated in the league but have again failed to see out a match away from home and come the end of the season this result, along with the 2-2 draws at Fulham, Aston Villa and Everton, may prove costly.
After the final whistle United manager Sir Alex Ferguson bemoaned referee Lee Mason’s failure to spot what he felt was a foul by Zigic on Rio Ferdinand in the build-up to the home side’s equaliser. He said: “Handball, a foul on the centre-half, he went right through him. If the referee can’t see that, what chance have you got?
“At this level, in a game of that importance, you hope you’re going to get a referee that can see that. If he can’t, what chance have you got?”
McLeish, however, insisted the goal was legitimate. He said: “It looks like it’s come off Zigic’s arm but it doesn’t look like he’s played it deliberately.
“It was in a melee of players and he was trying to keep the move alive and I think it would have been harsh if he had been penalised for deliberate handball.”
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news