Gates, 39, is the Chargers' career leader in receptions (955), receiving yards (11,841) and touchdown catches (116).
He did not play last season after he went unsigned as a free agent. He finished the 2018 regular season with 28 receptions for 333 receiving yards and two scores.
"After 16 seasons in the NFL, 16 seasons as a Charger, eight Pro Bowl appearances and many records broken, I find it hard to officially put this statement out and retire from the game of football," Gates said in a statement.
"I never dreamed that I would play this game of football so long or how fortunate I would be to play it with just one organization. ... While today I am officially retiring as a Charger, I am grateful that I will still be lending my services to the Chargers organization -- just now in a completely different capacity through the team's community engagement initiatives and public facing events."
Philip Rivers and Gates have combined for 89 touchdowns, the most in NFL history by a tight end-quarterback tandem.
"I remember like it was yesterday, the very first touchdown pass I threw him in Oakland in 2006," Rivers said. "We only threw 11 passes that day, and he wasn't quite as happy as I was after that TD. Who would've thought that many years later we would have the most touchdowns ever between a quarterback and tight end? I could go on and on about the memories from practice, games, the huddle, the sideline, the subtle in-game glances, the 'Come on now' as we broke the huddle which meant, 'Throw me the ball!' He was so hard to cover that we had a 'Gates Rule' in the QB room. We would talk through the reads and the plays and they all had a 'Gates Rule.' It pretty much meant, if he is one-on-one, throw it there."
Gates, a former college basketball standout at Kent State, is the league's career touchdowns leader among tight ends with 116. He is only the 22nd player in NFL history to catch at least 900 passes. His 955 receptions ranks No. 17 all time and third among tight ends.
"Antonio is not only one of the greatest Chargers to ever play the game, he's one of the greatest players in NFL history," Chargers owner Dean Spanos said. "His contributions to our organization over the course of an unprecedented 16-year career, both on the field and in the community, cannot be overstated. What he's meant to our family, to his teammates and to Chargers fans everywhere over the years -- there are no words. He's the best to ever do it at his position, and all that's really left is to start planning his Hall of Fame induction celebration in Canton. But for right now I simply want to say thank you, Antonio, and congratulations on a career for the ages."
Gates has posted 10-plus receptions in four games -- one of 11 tight ends in league history with at least four 10-catch games.
The Chargers were 53-40 in games in which Gates scored a touchdown.
Gates will become eligible for the Pro Football Hall of Fame in 2023.
ESPN's Eric D. Williams contributed to this report.