The move had been widely speculated and completes the on-field coaching staff for new Ole Miss coach Hugh Freeze.
Werner will coach quarterbacks and will serve as co-offensive coordinator along with offensive line coach Matt Luke.
Werner and Freeze coached together on the staff of former Ole Miss coach Ed Orgeron. Werner was offensive coordinator in 2006-2007, Orgeron’s last two seasons.
“We had to make sure that it was the right fit for my family and for the staff,” he told the Panolian newspaper. “It took awhile, but we felt this is the best for him and for me and my family.”