Last week, sources told ESPN that the 31-year-old was set to miss the tournament in Qatar.
The midfielder, who played a pivotal role in Les Bleus' winning campaign in 2018, suffered a setback in the final stages of his recovery last week and has now been ruled out for four months after the surgery.
Kante's early season has been marred by the hamstring problem that has now ruled him out of selection for the World Cup, which takes place from Nov. 20 to Dec. 18
Kante has featured in only two Premier League games and played a total of 175 minutes this season.
"The midfielder visited a specialist with the club's medical department to explore the options for his rehabilitation approach and it was mutually agreed for N'Golo to have surgery to repair the damage," Chelsea said in a statement.
Kante has been a vital player for Chelsea since his move from Leicester City in 2016 and equally important for France, having earned 53 caps.
Coach Didier Deschamps had warned that he would not pick any player who would not be fit for the start of the tournament.
Atleti said in a statement that Lemar "had to be substituted due to a muscular discomfort" and the team is pending on further exams to establish the severity of the injury.