The 29-year-old, who began his career at the Memorial Stadium, spent the final two months of last season back on loan with Rovers from the Valiants.
He played an instrumental role in the club’s return to the Football League and Rovers have now agreed a deal with Vale to bring him to the club permanently.
Boss Darrell Clarke told the club’s official website: “I know that Chris was keen on a return to his hometown club and his performances when he came back on loan last season proved that he had the ability to improve our squad.
“He quickly established himself in the side and I know how much helping us return to the Football League meant to him.
“He is an experienced player who knows the club well and I am delighted that he has returned to us on a permanent basis as we prepare for the season ahead.”
Lines added: “I think everyone knows that I have always been a Bristol Rovers supporter and I am so pleased to have this opportunity to play for the club again in the Football League.
“It was great being a member of the squad that got the club back up last season and to play at Wembley in the promotion final was an unbelievable experience.
“That’s all in the past now, though, and we have to prepare well during the summer to make sure we hit the ground running when the new season kicks off in August.”