The EFL said the parties were working to ensure an appeal could be heard tomorrow.
“Subject to the outcome, it could result in a further change to Saturday’s fixture,” the EFL said.
A member of the Southampton coaching staff was caught by Middlesbrough officials recording training on his phone.
The EFL confirmed further charges had been laid against Southampton, and that the club had also admitted observing training sessions ahead of matches against Oxford and Ipswich.
The first leg ended 0-0 before Southampton progressed with a 2-1 win after extra-time in the second leg.
Middlesbrough issued a statement welcoming the outcome of the disciplinary commission hearing.
“We believe this sends out a clear message for the future of our game regarding sporting integrity and conduct,” it said.