Scott was suspended last week following the incident, which came after a 3-0 home defeat at the hands of Blackpool.
He said: “I have enjoyed my five-and-a-half years with the club but, due to various circumstances, I believe it is in the best interests of the club, my family and myself that I depart and allow the club to move on.
“I wish the players and the club success on and off the field, and encourage them to now focus fully on climbing the League One table.
“I would also like to thank the chairman for his complete understanding of the recent events, and support over the time I was manager.”