The pair's one and only meeting came in a Saint-Etienne friendly five years ago, with Nigeria winning 1-0 thanks to a goal from Joseph Akpala.
This time around Les Bleus are heavy favourites, but Deschamps does have injury worries, especially in defence.
Victor Moses could take Babatunde's place in midfield, but the Chelsea man has also been hampered by a muscular problem.
The winner will take on either Germany or Algeria in Rio de Janeiro's Maracana stadium on Friday for a place in the semi-finals.
Possible starting lineups
France: Lloris; Debuchy, Varane, Sakho, Evra; Cabaye, Pogba, Matuidi; Valbuena, Benzema, Griezmann
Nigeria: Enyeama; Ambrose, Yobo, Omeruo, Oshaniwa; Mikel, Onazi; Musa, Moses, Odemwingie; Emenike
Sports Mole says: 2-0
Check out what the Sports Mole sofa panel think of the encounter below: