Sebastian Larsson gave Blues the lead from the penalty spot after Richard Dunne tripped Lee Bowyer, but Gabriel Agbonlahor brought Villa level before half-time with a clinical piece of finishing.
Zigic clinched victory for Birmingham in the 84th minute when his shot took a deflection off Luke Young and beat Brad Friedel.
McAllister said: "We feel hard done by. In the second half we were pressing to get the winner.
"It is disappointing to lose to a poor goal from our point of view. Now it is our job to pick everyone up in training and look to what is ahead."
Source: PA
Source: PA