The Celtic defender was issued with a notice of complaint by SFA compliance officer Vincent Lunny for "striking an opposing player, namely John Baird, with his elbow" during Celtic's 2-0 Boxing Day win at Dens Park.
He will miss the Clydesdale Bank Premier League game against Hearts at Celtic Park after the winter break on January 19 and the Scottish Communities League Cup semi-final against St Mirren at Hampden the following weekend.
Wilson contested the charge but it was upheld with the suspension applied with immediate effect.
The decision is sure to disappoint Wilson, who, was confident Baird's comments after the Dundee game would help his case.
Wilson said: "It wasn't an elbow so I don't know where the violent conduct has come from.
"To be fair the boy, he said he was grabbing my shirt and I was just trying to get away, which I was and unfortunately I caught him.
"If you go into a court of law and someone gives a statement like that then it is taken into consideration so I hope that is the case."
Meanwhile, Wilson today insisted it's vital the club retain the services of Gary Hooper beyond the January transfer window.
There are a number of English Premier League clubs tracking the Englishman with Liverpool and QPR already being linked with him. Newcastle are rumoured to be considering him as a possible replacement for Demba Ba after he signed for Chelsea last night.
Interest from the Anfield outfit could cool in the wake of their purchase of Daniel Sturridge but with Norwich City boss Chris Hughton also in the Parkhead stand yesterday, it appears as though there will be a host of clubs lining up bids during this month's transfer window.
Wilson said of the 18-goal striker who netted the only goal of the game in the 1-0 win over Motherwell: "Gary is a born goalscorer. That is what he does. If you get the ball to him inside the penalty area then more often than not he will get you a goal.
"Hopefully he will be staying here and remain fit because he is an important player for us as he showed yesterday with the winning goal."
Hoops boss Neil Lennon has already made it clear he has no intention of parting company with Hooper or midfield star Victor Wanyama, despite the fact the pair have been attracting plenty of attention on the back of their exertions for Celtic in the Champions League.
Wilson also paid tribute to goalkeeper Fraser Forster after he produced a wonderful penalty save to deny Tom Hateley.
With the scoreline locked at 0-0, it was his own mistimed tackle of Jamie Murphy which led to referee Steven McLean pointing to the spot.
He said: "You are always half-expecting big Fraser to make the save but it was a terrific effort to get across and keep it out.
"Obviously I was pretty relieved and I thanked him after the match. But he has done that on so many occasions for us this season. That is why he is now in the England squad.
"I think his performances this season have been outstanding and you need to remind yourself he is still only 24.
"He is probably the best keeper I have played in front of."
Celtic players will now take full advantage of the winter shutdown in the SPL by spending a week with their families before jetting off to Spain to a training camp.
And Wilson said: "It will be nice to get a break as we've played so many matches already this season.
"And it will be nice to spend a week training in decent conditions before coming back and focusing fully on the second half of the season and finishing strongly."