Simon Whaley scored the only goal of the game for the Lilywhites, but it wasn't enough to move Preston into the play-off zone as victories by Wolverhampton Wanderers, Southampton and West Bromwich Albion ensured it was they who finished inside the top-six.
It was all Preston in the first half with David Nugent having an early chance after five minutes when a 12-yard right-foot shot hit the post.
Two minutes later, Nugent was through again on the right-hand side of the penalty box and his cross shot was saved by the keeper's legs.
Gary McSheffrey fired over the bar from 15 yards with his left foot.
Nugent ran down the left wing and cut inside and had a 15-yard shot saved low down by the keeper diving to his right.
Sean St. Ledger was booked for a foul on Nicklas Bendtner and Sebastian Larsson had a 12-yard right-foot shot which hit the crossbar after Andy Cole's shot was blocked by Liam Chilvers.
Martin Taylor was booked for a foul on Nugent and Whaley had a great shot saved but Brett Ormerod couldn't score from the rebound.
Callum Davidson had a 25-yard shot saved just before half-time.
Birmingham made a change after the break when they replaced Bruno N'Gotty with Damien Johnson and it was the visitors who had the best chances in the second half.
Cameron Jerome replaced Andy Cole and Patrick Agyemang came on for Ormerod.
Preston captain Graham Alexander had a 20-yard right-foot shot saved and then Whaley did the same but he was booked for a dive in the penalty box.
Danny Pugh had a free-kick and a shot saved and Lewis Neal replaced Chris Sedgwick.
The only goal came five minutes from the end when Whaley latched on to a long ball and rounded Birmingham keeper Colin Doyle before scoring from close range with his left foot to send the Preston crowd ecstatic.
Jerome was booked for a foul on Preston keeper Wayne Henderson.
Michael Ricketts replaced Nugent - possibly making his last appearance at Deepdale - and had a shot saved by Doyle for a right-wing corner as Preston narrowly missed out on the play-offs.