Boniface did not train in Leverkusen on Tuesday and German media sources Bild and Kicker reported the forward was not on board when the plane departed to France in the afternoon.
On Sunday, Boniface was in an accident when a car he was travelling in collided with a truck on the autobahn.
On Sunday, the 23-year-old shared images and video on social media of a black Mercedes with a crumpled chassis along with images of his blood-soaked arm.
Leverkusen sporting director Simon Rolfes on Tuesday told reporters Boniface escaped serious injury but was in doubt for the clash.
"It's still open at the moment, a situation like this is not easy and he needs to get over it," Rolfes said.
"We're all very happy that nothing serious happened to him."
Boniface has seven goals in 10 games in all competitions this season. His likely replacement, Czech forward Patrik Schick, has one goal in eight games in all competitions.
