Innis will spend the 2015-16 campaign at Vale Park after impressing during a month-long temporary spell at the Sky Bet League 1 club last season.
The 20-year-old centre-half made five appearances for the Valiants but his stay was cut short by an ankle injury.
“Ryan is a very talented defender and someone we have been in talks with throughout the summer,” said Vale boss Rob Page.
“So we’re delighted to have added him to our squad ahead of the new season, which we’re hoping he will be a big part of moving forward.”
Inniss is a former England youth international and has previously had spells at Cheltenham, Luton, Gillingham and Yeovil.