The 35-year-old full back played for the 420th time for the Toffees in a 3-1 defeat to Bournemouth on the final day of the season.
He came on after 70 minutes to replace Lucas Digne. After the game, the Englishman announced he was hanging up his boots.
In a letter to Everton supporters on the club's website, Baines said: "I am incredibly proud to have represented Everton for the past 13 years and my decision to retire has been a difficult one to make.
"After speaking to my family, I feel now is the right time to end my playing career but I do so with many great memories at this proud football club.
"As someone from the city, Everton means so much to me and it has been an honour to be part of the club for so long.
"I would like to thank everyone who has supported me during my time at Everton, especially the fans who have been fantastic with me from the moment I signed."