Yates, who made 32 appearances in all competitions last season to help the Valiants win a first promotion in 19 years, has put pen to paper after agreeing terms a fortnight ago.
The 30-year-old former Crewe defender admits he never wanted to leave his home-town club.
"I'm over the moon," Yates told Vale's official website. "I have never wanted to leave this football club, I've stated that publicly a number of times, being a local lad it's just the icing on the cake to what has been a fantastic year for the club."
Yates follows Daniel Jones, Louis Dodds, Tom Morris, Chris Birchall and Sam Johnson in extending his stay at Vale Park, while Ben Williamson has agreed terms but has yet to sign.