The Plymouth Argyle boss lost his head during their 2-1 win over Blackburn last time out.
Rooney was left fuming after Rovers star Joe Rankin-Costello headed home an 86th minute equaliser, claiming their was a foul in the build-up.
The England and Manchester United legend lost his temper and was seen having a heated conversation with fourth official Jacob Miles.
He then called across referee James Linington, who sent Rooney to the stands.
But the side from Devon had the last laugh as Morgan Whittaker popped up with a 97th minute winner that saw them climb up to 14th in the Championship.
Rooney then returned to the pitch after the game to celebrate with his players and fans.
The FA revealed his punishment in a statement that read as cited by Sports Central: "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 admitted to this charge and an independent Regulatory Commission imposed his sanctions following a hearing."
He will now not been in the dugout tomorrow against Cardiff.
Opening up on the win over Blackburn and the sending off, Rooney told talkSPORT: "Me and the club secretary in the tunnel were celebrating, I broke his glasses celebrating. "So the win was a deserved win but sometimes it boils over a little bit and that's the nature of football. "It was my first time as a manager [getting sent off]. "I think as a manager or a head coach, decisions happen on the pitch and looking back, it's a free-kick, so the goal shouldn't have stood. "In the Championship you don't have VAR so the officials missed it and your emotions kick in and you know, I'm a passionate person, we want to win.
He added: "We worked extremely hard to win the game and to have that taken away by what I feel was a mistake by the officials, I felt was really harsh. "I reacted in a manner in which I shouldn't have and the red card was deserved. "From my point of view the fans were fantastic, it almost galvanised the players and the stadium and we kept pushing to get the winning goal."
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