That prompted boss Gus Poyet to withdraw the offer of a new deal to Calderon, who joined Brighton as a free agent in January.
But he has now signed a contract which Brighton can cancel after six months if he fails to recover from a hip injury he suffered in April.
Calderon told the club website: "I am pleased everything has been sorted out and that I have now signed a long-term deal with the club.
"I had wanted to talk to Southampton although my mind was virtually made up.
"My heart is with Brighton & Hove Albion. I love the city, the fans and the club and ultimately did not want to leave."
Source: BBC Sport
Source: BBC Sport