Referee Bobby Madden booked the full back after judging he had dived in the penalty area at Tannadice as the Dons ran out 1-0 winners.
As the move continued, Aberdeen fired the ball into the net only for the official to blow his whistle and award a free-kick to United.
Dons boss Derek McInnes was sent to the stands for protesting against the decision and faces a Scottish FA hearing over claims he used "abusive and insulting language" towards Madden.
The Scottish FA confirmed Shinnie's yellow card has been rescinded and will be wiped from the player's record.