Jones was charged by the Football Association with improper conduct for his post-match comments at Bristol City last week.
The charge was upheld at Thursday's disciplinary hearing, triggering a one-match suspended ban hanging over the Wednesday boss since a touchline bust-up at Brighton earlier this year.
A further one-match suspension was imposed, consigning Jones to the stands for his side's forthcoming games against Leeds and Blackpool.
Bristol City's last-minute equaliser at Ashton Gate was the source of Jones' anger.
He said at the time: "It was a forearm smash by Marvin Elliott. Anywhere else on the pitch, it would have been a free-kick.
"We had taken everything City could throw at us and all you ask is a fair deal from the match officials.
"We have had trouble with this referee (Darren Deadman) before. If he had done his job we would have been going home with three points, but I get tired of saying that sort of thing."