Brazil were trailing to a Darwin Nunez opener when Neymar landed awkwardly after colliding with Nicolas de la Cruz just before half-time.
After De la Cruz made sure of Uruguay’s win, Neymar was reportedly seen leaving the Estadio Centenario in Montevideo on crutches.
“Let’s hope it’s nothing serious,” Brazil captain and Manchester United midfielder Casemiro said on Globo television.
“He’s an important player for us, we’re very fond of him. He’s been suffering a lot from injuries and when he starts to pick up the pace he gets injured again.”
Elsewhere, Lionel Messi became the all-time leading scorer in South American World Cup qualifying as he bagged a brace in Argentina’s 2-0 victory over Peru.
Messi’s 31 goals take him clear of former Barcelona team-mate and Uruguay forward Luis Suarez, who has 29. Argentina top the qualifying table having won all four fixtures.