The defender has been coming on leaps and bounds over the last couple of seasons, helped by going out to the Stadium of Light for a couple of loan spells, the team he made his 64th appearance for United against on Sunday.
Confirmation about the deal will come in the next couple of days.
"Jonny has proved himself," Said Ferguson to MUTV.
"He has signed a new contract and helps to provide a good foundation for the club for a long time."