Manning is considered one of the most popular and most decorated players in Giants history and led the team to two Super Bowl championships.
"For 16 seasons, Eli Manning defined what it is to be a New York Giant both on and off the field," said John Mara, the Giants' president and chief executive officer. "Eli is our only two-time Super Bowl MVP and one of the very best players in our franchise's history. He represented our franchise as a consummate professional with dignity and accountability. It meant something to Eli to be the Giants quarterback, and it meant even more to us. We are beyond grateful for his contributions to our organization and look forward to celebrating his induction into the Giants Ring of Honor in the near future."
The recently turned 39-year-old's future had been in doubt since the end of the season. Manning's contract with the Giants expired after the 4-12 season and there was little chance he would be returning after losing his long-time starting job to rookie Daniel Jones.
Manning said he wanted to think about his future after the season and roughly three weeks after the season ended he decided his career was over.
The Giants said Manning is one of the most accomplished players in the 95 seasons of Giants football. He is the only player in franchise history to suit up for 16 seasons and his 236 regular-season games (234 starts) and 248 total games are both Giants records.
"Here goes the retirement of a great, great football Giant," said Tom Coughlin, the Giants' head coach from 2004-2015. "I and my coaching staff and our teams from 2004 right through 2015, for me at least, my part, hold Eli in the highest respect and congratulate him and his family, and his mom and dad, for all of the wonderful, wonderful experiences he's had, and the happiness and pride that he has brought to the entire Giants family, the fanfare, the fans, the family and everyone that's taken so much pride from his performances and for what he's meant. He's always been there to make the call, to stand up and represent the Giants in the best possible way."
Manning is one of just five players in NFL history to win multiple Super Bowl MVP awards, joined by Brady, Joe Montana, Terry Bradshaw and Starr. Manning is one of 21 quarterbacks to win a Super Bowl without losing one and one of 12 to win at least two Super Bowls.
In the 2004 draft, the Giants picked fourth and selected quarterback Philip Rivers. Accorsi sent Rivers, their third-round choice in 2004 (No. 65 overall), and first and fifth-round picks in the 2005 draft to the Chargers for Manning.
It was the game-changing deal for the Giants.
The official Twitter account for the NFL said Manning's retirement marks the end of an era.
(The Associated Press contributed to this report.)