The 31-year-old left-back, whose contract expires at the end of the season, has made 240 appearances for the Saints, scoring eight goals, since his initial loan from Chelsea was made permanent in February 2015.
Bertrand reached the FA Cup final, two FA Cup semi-finals and was part of the team that secured the club's highest finish in the Premier League in the 2015-16 season.
'Time to respectfully part ways'
Southampton said in a club statement: "Whilst that time will always be fondly remembered, the club and Ryan have agreed that now is the time to respectfully part ways and move forward on different paths."
In a social media post, Bertrand dismissed reports he had rejected a new contract offer from Southampton as inaccurate.
'Many months of hard decision making'
"After many months of hard decision making, I have decided to leave Southampton Football Club," he said.
"This has only been decided in the last 48 hours and comments that I had not accepted an offer previously are not true."
Bertrand, who has made 34 appearances for Ralph Hasenhuttl's side this season, has recently been linked with a number of clubs, including Arsenal.
'Seek a new challenge'
"This has been a difficult decision for me, but the time has come for me to seek a new challenge and find a new home that allows me the freedom to play and maximise my contribution to the team," added Bertrand, who has won 19 caps for England.
With Bertrand having missed the club's last three matches through injury, he will be hoping to be back fit to make one last contribution.