The 31-year-old, who joined Saudi Arabian side Al Hilal from Paris Saint-Germain in August, was stretchered off in tears just before halftime in Brazil's 2026 World Cup qualifying match in Montevideo Tuesday.
Neymar will undergo surgery for the injuries at a "yet-to-be-determined date," the CBF said, after a series of medical exams on the player in Sao Paulo.
"Brazilian and world football need Neymar healthy and recovered because football is happier when he's on the pitch," CBF president Ednaldo Rodrigues said in a statement.
The CBF said its medical department and Al Hilal are in "constant contact" and "aligned" on helping the striker recover.
Neymar, who overtook Pele as Brazil's all-time top goal scorer last month, twisted his knee in a collision with Uruguayan midfielder Nicolas de la Cruz in stoppage time near the end of the first half.
Carried off on a stretcher, he left the stadium on crutches and wearing a leg brace after the match.
It is the latest in a string of injuries for the star, who underwent surgery in March for an ankle problem that sidelined him for six months.
Fitness problems overshadowed much of his six seasons at PSG, which signed him for a world-record $234 million (222 million euros) in 2017.
He signed for Al Hilal for a reported $95 million in August.
Knee injuries are among the most common and serious in football.
The CBF said Neymar's injury was to his anterior cruciate ligament, one of the worst of all.
Surgery to repair the condition often takes players out of action for months.