The 29 year old, who returned to his former club on loan in March, quickly became an influential member of the squad, featuring in the club's remaining eight league matches and the play off semi final games against Forest Green Rovers and the Promotion Final against Grimsby Town.
Chairman Nick Higgs was delighted to have finally got his man following protracted discussions with Port Vale, where Lines still had one year of his contract to run.
"We have been talking with Port Vale for a number of weeks and I am very pleased that we have now reached an agreement whereby Chris can return to us on a permanent basis.
"His performances for us at the end of last season, when he came back to the club on loan, were outstanding and he always stated that he would like to return to us on a permanent basis if the opportunity arose.
"We saw a more mature, experienced, player who had benefitted from his time with Sheffield Wednesday, MK Dons and Port Vale after he left us back in 2011 and his experience will be invaluable to us now that we have returned to the Football League.
"I know that our supporters will be delighted to have Chris back with us on a permanent basis and I would like to formally welcome him 'home' and wish him every success in the coming season."
Manager Darrell Clarke said that Lines was an ideal signing for the club; "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, who scored one of the all important penalties in the Wembley shootout against Grimsby, said; "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."