Scottish FA chief executive Stewart Regan met match officials on Monday.
"I can confirm that Steven Craven has tendered his resignation and will no longer officiate in the professional game," said Regan.
"I hope to conclude the investigation within the next 48 hours and will make further comment at that time."
Celtic boss Neil Lennon was furious that Dougie McDonald, the referee in the game on 17 October, first awarded a penalty then changed his mind after consulting with his assistant, Craven.
The match officials were subsequently praised by the SFA's head of referee development, Hugh Dallas, for getting the decision correct.
Hooper scored a last-minute goal to win the match for Celtic.