O'Connor tussled with Latics player Hallam Hope in the 70th minute of City's 2-0 loss in the League Two fixture on Feburary 19 and it led to an unseemly fracas involving a number of players from each side.
City won their appeal against the dismissal of O'Connor.
Both clubs accepted the fine for breaching FA Rule E20.1.
An FA statement read: “Both admitted they failed to ensure their players conducted themselves in an orderly fashion and/or refrained from provocative behaviour during the 70th minute of the fixture.”
Last month, Barnsley and Cardiff City were also fined by the governing body following heated scenes after their Championship encounter at Oakwell on February 2.
Players and coaches from both sides clashed shortly after the final whistle of Cardiff's 1-0 victory.
The FA "alleged that both clubs failed to ensure their players and/or club officials conducted themselves in an orderly fashion and/or refrained from provocative behaviour".
Barnsley, who admitted their charge, have been fined £12,000. Cardiff denied their charge but were fined £10,000.
An independent regulatory commission found the charge against Cardiff to be proven.