The nature of the injury was not revealed but Coufal returned to the side to face Brentford in the League on Sunday.
The Czech squad does include two other Hammers in midfielders Tomas Soucek and Alex Kral.
As well as Coufal, the Czechs suffered more loses today with the Slavia Prague trio of defender Jan Boril and midfielders Lukas Masopust and Petr Sevcik pulling out due to injury.
The Czechs have collected seven points from five matches in Group E, level with Wales but sitting in second place on goal difference behind runaway leaders Belgium.
After hosting Wales on Friday, the Czechs travelling to face Belarus on October 11. Wales are without captain Gareth Bale due to a hamstring injury.