Atsu was forced to withdraw after 14 minutes of the Group F clash in Egypt and could miss the Black Stars' final group match against Guinea Bissau on Tuesday night.
The 27-year-old winger was replaced by Samuel Owusu and faces a scan to determine the extent of his injury.
Ghana remain in second place on two points - two behind holders Cameroon - after a 2-2 draw against Benin in their opening fixture and a victory against Guinea Bissau will secure their place in the last 16.
Atsu played a significant role for the four-time African champions in their run to the 2015 final, winning the Best Player and Goal of the Tournament, losing to Ivory Coast on penalties.