The 35-year-old, who had one year remaining on his contract at Roots Hall, has hung up his boots due to a persistent knee injury and has been linked with a coaching role at former club Millwall.
He told the Shrimpers' website: "I thoroughly enjoyed my time at Southend United and realised a boyhood dream by playing for the club I used to watch from the North Bank.
"I enjoyed every minute of my time at Roots Hall but unfortunately due to injury I have had to end what has been a very enjoyable career. I am now looking ahead to the future and the rest of my life."
New Millwall boss Steve Lomas is currently deciding on his backroom staff and could turn to club legend Harris, who scored 138 goals in two spells at The Den.