Ferdinand and his team-mates were incensed at Cakir's decision to show winger Nani a straight red card on 56 minutes for catching Alvaro Arbeloa in the chest with his raised studs.
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Sir Alex Ferguson was described as "too distraught" to face the media in the wake of the defeat, with assistant Mike Phelan taking his place.
But Uefa has come out publicly in support of Cakir, and Ferdinand could be handed a ban for the gesture if the referee or match delegate reference the incident in their reports of the game.
Ferdinand's outburst is merely the latest in a long line of incidents involving sarcastic applause.
Only last month, Luis Suarez was cautioned in the dying minutes of Liverpool's Premier League clash with West Brom for applauding Jon Moss after the referee awarded the Baggies a free kick.
In September 2005, Wayne Rooney was handed a two-match ban for clapping and swearing at official Kim Milton Nielson during a Champions League encounter between United and Villarreal.