Alan McLoughlin rescued Portsmouth with a highly controversial penalty three minutes from the end after Birmingham had recovered to take the lead.
McLoughlin converted his second spot kick of the match after referee Steve Bennett had decided substitute Steve Lovell had fallen over Martin O'Connor's attempted clearance.
Mr Bennett was surrounded by angry Birmingham players as he pointed to the spot-kick and McLoughlin made no mistake as he gave Portsmouth a share of the points which had looked beyond them earlier.
Portsmouth had the better of the first half but Birmingham recovered after manager Trevor Francis had made an important double substitution at the interval.
Francis sent on Dele Adebola and Stan Lazaridis, both back from injury, and the match was transformed.
McLoughlin gave Portsmouth the lead in the 35th minute with the first of his penalties, though Birmingham had no complaints about its award.
Gary Rowett appeared to hold down Guy Whittingham as they competed for a centre from the right and McLoughlin stepped up to score the penalty.
But after the break Birmingham were a different side and Adebola almost equalised in the 55th minute with a shot from 15 yards which was finger-tipped to safety at full stretch by goalkeeper Andy Petterson.
But there was nothing Petterson could do about Birmingham's equaliser in the 59th minute when O'Connor put Lazaridis away on the left and the Australian cut in onto his right foot to beat Petterson with a fierce shot from the edge of the area.
Portsmouth were still reeling when Birmingham scored a soft second goal in the 62nd minute.
Lazaridis took a corner on the right and defender Michael Johnson was unmarked from 10 yards when he headed in.
Birmingham almost scored a third in the 79th minute when from a free-kick on the edge of the area Lazaridis struck the angle of post and bar.
After the award of Portsmouth's second penalty Birmingham were reduced to 10 men when defender Darren Purse was sent off.
Purse got a second yellow card for a foul on Lovell and there was the bizarre sight of a red card being brandished at him by referee Bennett as he was carried off on a stretcher nursing a foot he hurt in committing the foul.