The Japan international was taken ill before the Newcastle match on Saturday 7 December, but after playing against Shakhtar Donetsk he was then absent for the trip to Villa Park on Sunday.
"Shinji's sick. He still hasn't recovered physically from the sickness he had. He's just not right," Moyes reported after the 3-0 win on Sunday.
Chris Smalling and Marouane Fellaini could be in the mix for Wednesday night's Capital One Cup quarter-final at Stoke. Speaking ahead of the trip to Villa, Moyes had said the pair were "getting closer" but neither made the substitutes’ bench at Villa Park.
Robin van Persie's thigh injury means the striker misses around one month, but Michael Carrick is closing in on a return to contention after an Achilles tendon problem.