The former Wales international rejoined the club last July, scoring four goals in 34 appearances in the 2013-14 season.
Tranmere's football operations director Mick Horton told the club's website: "We are delighted Jason has agreed to lead our attempts to make an instant return to League One.
"He showed his dedication to the club by playing on in the last weeks of the season, despite carrying a toe injury that left him limping for days.
"His presence in the dressing room will also be invaluable as we look to introduce young players to the team next season."
Tranmere will play in League Two next season after finishing last campaign 21st in League One.