The Reds denied the charge issued by the FA earlier this week and had been hopeful of McGeehan being cleared, feeling that the midfielder showed no malicious intent.
But an independent regulatory commission has upheld the decision, with Barnsley 'exceptionally disappointed' by the verdict.
McGeehan was alleged to have been involved in an incident in the 54th minute of Saturday's League One match at Southend United when he challenged home defender Sam Hart - which was picked up by the TV cameras in the game, televised on Sky Sports.
A statement read: “Cameron McGeehan will be suspended for Barnsley’s next three matches. The midfielder denied a charge of violent conduct, which followed an incident not seen by the match officials but caught on video in the 54th minute against Southend United on March 2 2019, but it was subsequently found proven by an Independent Regulatory Commission.
"Barnsley Football Club are exceptionally disappointed in the decision to suspend McGeehan after the charge was denied and a clear explanation was given.
"The club offered the view that the video evidence shows the opposition player moving whilst on the floor, when McGeehan was unable to change the course of his direction in mid-air. There was no complaint from the opposition players, staff or the officials at the time despite it being in front of both dugouts. An apology was then instantly offered and accepted from each player involved.
"The games McGeehan will miss are Accrington Stanley (H), Sunderland AFC (H), Doncaster Rovers (A)."