Julian Gray and Emile Heskey twice put Birmingham ahead but Alan Dunne and Elliott gave the home fans hope of causing an upset for Peter de Savary's first match as Millwall chairman.
De Savary was introduced to the home fans before the match and in a toe-curling address promised the supporters to lead the side to promotion.
And the new chief's comments - which ended with a plea to 'Give a roar for the Lions' - seemed to have an effect on the players as they made a bright start against their Premiership opponents.
The ill-feeling between the two sets of fans, stemming from the riots outside the Den following the play-off semi-finals in May 2002, was obvious from the outset.
And in the eighth minute of the match the police were called into action to stop a group of home fans from getting near the away stand.
Three minutes later Gray opened the scoring for Birmingham as he latched on to Heskey's cross from the right to fire past Lenny Pidgeley.
Jermaine Wright should have equalised for Millwall on 25 minutes after Dunne had taken advantage of a mistake by Martin Taylor, but the winger scuffed his shot across the face of goal.
On loan keeper Pidgeley made two excellent close-range saves in quick succession in the 32nd minute, first keeping out Heskey's header then denying Matthew Upson from the resulting corner.
Then Dunne levelled on 57 minutes after beating Walter Pandiani near the edge of the area before curling in a shot from a tight angle which went in off the crossbar with Nico Vaesen well beaten.
Heskey had two chances to win the game in the second half but fired wide from 20 yards on 61 minutes, before letting his shot drift the wrong side of the far post with an empty goal begging.
But Millwall looked determined to win in normal time and Ben May should have done better with his 80th minute volley which flew wide of the near post.
He then set up Elliott for a long-range shot which whistled past the post with Vaesen looking on helplessly.
Heskey made up for his earlier misses five minutes into extra time but Elliott sent the tie to penalties with three minutes left with a thunderous strike from 25 yards to send the fans into delirium.