The 20-year-old made 11 appearances in all competitions last season and will now remain at Roots Hall until 2016.
Bentley, who joined the Shrimpers' youth system following his release from Arsenal in 2011, is already a firm favourite at the club for his penalty heroics in both the FA Cup and Johnstone's Paint Trophy against Bury and Oxford last term.
"I really enjoyed last season, especially the penalty shootout wins and of course keeping my first-ever professional clean sheet," he told the club's official website.
"But my aim this season is to build on that and hold down the number one shirt. Obviously Paul Smith has been out injured in pre-season but we will both push each other this season to be starting on a Saturday.
"The new deal means I'll be with the club until at least 2016 and it's great it has all been agreed."