It seemed as if Dimitar Berbatov's sublime goal in the 58th minute had wrapped up all three points for United but Bowyer salvaged a share of the spoils in controversial fashion a minute from time.
There was a suspicion of handball when Birmingham striker Nikola Zigic got to Roger Johnson's cross.
The ball then rebounded to Bowyer - whom United were convinced was offside - and he slid in to score a goal that ensured Birmingham, briefly in the relegation zone, climbed out of the bottom three.
It took United unbeaten in the league this season, nearly an hour to pierce Birmingham's defence before Berbatov started and finished a fine move that saw the Bulgaria striker score his 14th goal of the season.
By contrast, Wayne Rooney was left searching for his first goal in open play since March after yet another frustrating match for the England striker.
Earlier Mario Balotelli scored a hat-trick as second-placed Manchester City, now level on points with United, who have two games in hand, won 4-0 at home to Aston Villa.
"We did a good job," City manager Roberto Mancini said.
Mancini revealed that Balotelli, his fellow Italian, was suffering from homesickness as he denied reports the striker wanted to leave Eastlands.
"He's only 20-years-old. It's the first time he goes away from home. But he's happy, maybe missing his family, but everything is fine."
Tottenham Hotspur meanwhile displaced Premier League champions Chelsea in the top four after a 2-0 win at home to Newcastle.
England international Aaron Lennon's second-half goal broke the deadlock at White Hart Lane.
Then, for the second match in a row, Spurs were reduced to 10 men when Younes Kaboul was sent off in the 65th minute after his head needlessly made contact with Newcastle's Cheik Tiote.
But, as was the case in their win over Villa, Spurs scored a second goal when a man down with in-form Wales midfielder Gareth Bale netting nine minutes from time.
"We are disappointed with the sending off, you don't do something that silly, but the lads were fantastic after that," Spurs boss Harry Redknapp said.
Blackpool's fairytale first season in the Premier League continued with a 2-0 win away to Sunderland secured by striker DJ Campbell's second-half double.
"They amaze me week in and week out," Blackpool manager Ian Holloway said of his side, who have defied all pre-season forecasts to be in eighth place.
"We rode our luck a little bit but we are absolutely delighted," he added after Blackpool inflicted Sunderland's first home league defeat of the season. "I can't thank the lads enough for their efforts. I'm on cloud nine."
At the other end of the table, Fulham climbed out of the bottom three after a 2-0 win away to Stoke City where defender Chris Baird scored twice for his first goals in four years.
It was only Fulham's third league success this season and their first away victory in the Premier League since August 2009.
"I thought we were good value, everybody stood up and was counted," said Fulham manager Mark Hughes.
Nikola Kalinic scored twice but was then sent off as Blackburn Rovers won 3-1 away to West Bromwich Albion.
West Ham, who climbed off the bottom of the table by beating Fulham on Sunday, remained in the relegation zone after a 1-1 draw at home to Everton.
Tony Hibbert's 16th minute own-goal gave the Hammers the lead before Everton's Seamus Coleman levelled three minutes before half-time.
Chelsea, looking to bounce back from their 3-1 London derby defeat by Arsenal on Monday, face Bolton on Wednesday when the Gunners travel to Wigan and Liverpool welcome Wolves to Anfield.