Dimitar Berbatov had followed his double in the Boxing Day win over Sunderland with what looked another decisive contribution to take his tally for the campaign to 15 goals.
But Bowyer, who had scored the winner against Chelsea last month, equalised to lift Birmingham out of the bottom three.
United's point enabled them to move ahead of Manchester City on goal difference - they also have two games in hand - and nudge seven points clear of champions Chelsea.
They are now unbeaten in 23 league games and have lost only two of 36 Premier League matches during the calendar year.
Arsenal could overtake them with a big win at Wigan tomorrow, but the likelihood is United will be top at the start of January.
Sir Alex Ferguson's side were not at their best but still looked to carry too much guile for Alex McLeish's home side before their late show.
Berbatov made an early run into the Birmingham box but Sebastian Larsson was alert to the situation and halted United's leading scorer.
Larsson then showed his attacking prowess with an inviting cross from the right flank, but Cameron Jerome was unable to keep his header down and it flew harmlessly over the bar.
Wayne Rooney, without a club goal in open play since March, tried his luck from 25 yards out but his shot was a couple of yards off target.
Rooney was then found to the left of the box by Anderson but, after cutting inside Stephen Carr, he curled a shot straight at former United goalkeeper Ben Foster.
United went close to breaking the deadlock after 18 minutes after Anderson released the overlapping Ryan Giggs.
His cross-cum-shot almost deceived Foster but he managed to finger-tip the ball on to his right-hand post.
Michael Carrick gave away a free-kick when he jumped into the back of Jerome 20 yards out but Larsson curled his shot just wide.
United's Anderson was then yellow-carded after being involved in a spat with home midfielder Barry Ferguson. City midfielder Craig Gardner also joined in and was booked by referee Lee Mason.
Then Bowyer went into the notebook after a late challenge on Darron Gibson who was starting his first league game since April.
Nemanja Vidic picked up the fourth yellow card of the match for chopping down Jerome as he bore down on goal in a central position.
Gardner's free-kick was deflected wide as Birmingham started to gain a foothold in the match by lifting the tempo.
Gardner was only just off target with a swerving low drive which had Edwin van der Sar scrambling across his line.
Bowyer then teed up the former Aston Villa player 20 yards out but his shot was off target.
Birmingham, beaten at home only once in 16 months, started the second half in positive fashion.
Larsson sent a flick header across the face of goal from Jerome's cross after good play by Beausejour.
Bowyer had a shot deflected for a corner and then Gardner volleyed straight at Van der Sar from 12 yards.
Then after 58 minutes Berbatov broke the deadlock.
Gibson played a probing pass into the path of the striker who came inside Liam Ridgewell before drilling a low shot past Foster into the corner of the net.
It was his eighth goal in his last three starts.
The Bulgarian almost added a second goal two minutes later when his low shot beat the dive of Foster and clipped the outside of a post.
McLeish made his first change after 68 minutes with fit-again Alexander Hleb replacing Larsson.
Darren Fletcher replaced Anderson in United's first change after 72 minutes.
Blues defender Scott Dann was yellow-carded for a late challenge on Berbatov, and Foster then reacted well to turn over a powerful Vidic header from Giggs' corner.
McLeish brought on Nikola Zigic and Kevin Phillips in place of Beausejour and Jerome respectively.
Foster reacted well to turn over a powerful Vidic header from Giggs' corner.
But there was still time for a twist, and with a minute remaining in regulation time Bowyer rescued a point for Birmingham when a deep cross from Johnson was helped on by Zigic, with a hint of handball, and fell into the path of the former England midfielder who made no mistake.