Rooney was charged for his behaviour in an eventful win over Blackburn where he was sent off for allegedly insulting the fourth official and returning to the pitch after his dismissal.
Plymouth were leading 1-0 when Blackburn scored an equaliser in the 86th minute which Rooney and his players felt should not have stood, with the former Manchester United and England forward seen fuming at the fourth official.
Referee James Linington gave Rooney a red card and he walked down the tunnel at Home Park but was back on the pitch to celebrate a 97th-minute winner from Morgan Whitaker.
"Wayne Rooney has been given a one-match touchline ban and 5,500 pounds ($7,180.25) fine for misconduct at Plymouth Argyle's EFL Championship match against Blackburn Rovers on Saturday 5 October," the FA said in a statement.
"It was alleged that the manager's conduct around the 87th minute was improper and/or he used abusive and/or insulting words towards a match official, which led to his dismissal.
"It was further alleged that following his dismissal his conduct was improper and/or violent. It was also alleged that by returning to the field of play after being dismissed his behaviour was improper."
Rooney was appointed Plymouth manager in May. They are 14th in the standings before visiting Cardiff City on Saturday.
