The 29-year-old has been at the club since 2011, and has now put pen to paper on a deal which will extend his stay until 2025.
"I'm very pleased. It's nice to get it all sorted before the season starts and just allows me to focus on the football and hopefully have a positive season," he told the club's official website.
"I think over the summer there was a lot of uncertainty over what was going on.
"But I had some good conversations with the manager and he made it clear that he wanted me to stay and I've loved working with him these first few weeks and I'm really confident that we're going to have a good season, so it was an easy decision for me to sign the contract and I'm really happy."
Director of Football Jason Wilcox added: "Jack is an integral part of the club and having been here for 12 years, his loyalty is extremely valued by us.
"His leadership makes him a key part of our rebuilding project and Jack will play a telling contribution both this season and beyond.
"I'm delighted he has signed this new contract and bought into the vision we have under the guidance of Russell Martin."
Stephens has made 151 appearances for the club since his debut as a 17-year-old, but spent last season out on loan at Bournemouth as Southampton suffered relegation from the Premier League.
The Saints will begin their new Championship campaign - and life under new manager Russell Martin - against newly-promoted Sheffield Wednesday in the first game of the 2023-24 EFL season this evening.