Goalkeeper Richard Kingson's horrendous blunder and a superb strike from Niko Kranjcar piled on the misery for managerless Birmingham and kept Harry Redknapp's side on course for a European spot.
Caretaker manager Eric Black gambled on dropping the experienced Maik Taylor but the move backfired as Kingson - on his Barclays Premier League debut - allowed a shot from Sulley Muntari to slip under his body.
Then Kranjcar, scorer of Croatia's first goal against England via Scott Carson's blunder in midweek, drilled home a superb free-kick with eight minutes remaining.
It clinched a fifth successive away win for Pompey and extended their unbeaten league run to nine games to keep them in the top six.
But Birmingham, who had beaten Pompey 5-0 when they last met at St. Andrews two seasons ago, have now lost six of their last seven league games and are sliding rapidly towards the relegation zone.
Portsmouth always looked as if they possessed more fire-power than the home side and have now scored 14 goals in eight matches away from Fratton Park.
Black is in the frame to move into the managerial hotseat along with Scotland boss Alex McLeish - his former Aberdeen team-mate - after Steve Bruce's departure and he could not fault the commitment of his side.
But there was a lack of quality and cutting edge in the final third of the field where Sol Campbell and Sylvain Distin dominated for Portsmouth.
Only 22,089 witnessed the first match since Bruce's departure and Blues could be in for a bleak winter unless prospective new owner Carson Yeung invests heavily in January - if and when he finally takes control.
The home side, who gave striker Mikael Forssell a first start for nearly three months, made a bright start without really threatening to break the deadlock.
The first worthwhile save came after 15 minutes when Kingson, whose only previous appearances had been in the Carling Cup, did well to turn aside a fierce curling drive from Sean Davis.
James produced a superb low save after 20 minutes to keep out a shot on the turn from Forssell after he had brought down a first time cross from Schmitz.
Then after 33 minutes a terrible error by Kingson allowed Muntari to give Pompey the lead - his second goal of the campaign.
Pompey's leading scorer Benjani Mwaruwari picked out the run of the midfielder and, although he got his shot on target, it should have been comfortably dealt with by Kingson.
But the former FC Hammarby player allowed the ball to slip through his arms and squirm under his body into the net.
Birmingham tried to retaliate and it needed a good tackle by Sylvain Distin to halt Kapo just inside the box.
The home side appealed in vain for a penalty after a challenge on Forssell by Sol Campbell and, as the ball broke to Mehdi Nafti, he fired in a low shot which James saved at the second attempt.
Sean Davis became the first player to be yellow carded after 38 minutes for a challenge on Forssell.
Kingson looked shaky after his blunder and he sliced a back pass from Johan Djourou out of play under no pressure.
Black saw a positive response from his side at the start of the second period and McSheffrey picked out the run of Forssell but Distin was alert to the situation with a sharp tackle.
McSheffrey then broke forward with Birmingham having a four versus three advantage on the counter-attack but his low cross was gathered by James.
The England 'keeper raced out of his area to head clear from Forssell but City had a let-off when Pamarot shot over from 12 yards out after Utaka had made the break into the box.
Muntari had a first time shot deflected wide by Stephen Kelly from a low pass from Utaka.
James was again alert to save at the feet of Kapo from a fine pass from Muamba. But Pompey always threatened on the break and Kingson was well positioned to hold onto a low drive from Benjani.
With eight minutes left Kranjcar wrapped up the points for Portsmouth with a stunning free-kick.
