The former England man was dismissed by referee Daren Drysdale for a last-minute foul on Cameron Park and former Robin Leroy Lita scored the penalty to seal a 4-0 win for Boro.
But City boss Keith Millen has appealed after viewing the incident.
He said: "Liam Fontaine was back on the line and the player's touch actually took the ball towards two other defenders.
"It's also debatable if David James even touched their lad and David was adamant that he hadn't fouled him.
"We think it's only right we appeal the decision and we'll be sending the footage off to the FA."
Source: PA
Source: PA