The Volyn midfielder was struck on his right arm by the ball when he got in the way of Ogenyi Onazi's shot just after the hour mark and needed medical attention.
Nigeria lost the match but the African side still claimed a place in the knockout phase of the FIFA World Cup.
Babatunde will play no further part in the tournament, though, after undergoing an operation on his arm.
Nigeria did confirm, however, that the 21-year-old midfielder has returned to the team's training base in Campinas, rather than returning home or back to his club in Ukraine.
A comment from their official Twitter account read: "Babatunde Michael has undergone a successful surgery on his fractured wrist and has since returned to the team's Camp base in Campinas."
Nigeria will face France in the second round in Brasilia on Monday.
