It had looked like Neil Danns' second-minute free-kick would give Palace only their second away win of the season in the npower Championship, but Julian Speroni brought down Danny Rose and Pitman converted the 94th-minute spot-kick.
Danns gave Palace the perfect start. The midfielder was pulled down by Khalifa Cisse on the edge of the area, he got up and beat David James all ends up with his shot finding the top right-hand corner.
Palace should have gone 2-0 up when Pablo Counago played a neat one-two with Sean Scannell but the Spaniard put his shot wide.
Millen responded by boosting his firepower with the introduction of Pitman, Rose and David Clarkson, but City struggled to create chances in the second half.
Rose had an effort blocked after 77 minutes but it was not until the 85th minute that Palace keeper Speroni was called into action to tip over a shot from Adomah. The Palace goalkeeper then conceded the penalty and was unable to make amends.