The 28-year-old played a prominent role in The Seagulls' promotion from Division Two and is delighted to have agreed an extended stay on the South Coast.
"I love Brighton as a place and I've really settled in at the club. I'm delighted to be staying and looking forward to a new challenge in Division One," said Jones.
"I have really enjoyed the last two years and no one could be happier than me after getting this contract."
Jones arrived at The Withdean from Southend on a free transfer in June 2000 and has enjoyed two successive promotions with the club.
Former boss Peter Taylor was keen to seal the deal with Jones, and the conclusion of the negotiations follows the likes of Shaun Wilkinson, Daniel Marney, Will Packham and Paul Rogers, who have all agreed new contracts with the club.
