School leaders appealed the case but were turned down on Wednesday.
Jones administrators apparently failed to file a hardship waiver following the QB's transfer from another school.
"He feels horrible what happened, Jones having to forfeit games, but you can't blame him. He didn't do it," said attorney Scott Adams.
Attorney Adams did negotiate a deal for the player at the heart of the dispute.
He'll now transfer to another school and will be allowed to play next season.