Antonio Conte has made the left-back one of his first-choices in his five-man defensive system, moving the player to a more central position.
Davies featured for 90 minutes in Thursday’s 2-1 win over Austria and will sit out the friendly against Czech Republic on Tuesday after departing from the Welsh team.
The reason behind his withdrawal was not revealed in an FAW announcement on Sunday.
A statement read: “Following Thursday’s match, Ben Davies has returned to his club. All other players are available for Tuesday’s match.”
The victory in Cardiff put Wales within a game of the World Cup in Qatar, although their play-off final will not take place until June following the postponement of Scotland’s game against Ukraine.
Tottenham face Newcastle on Sunday, April 3, with a three-point deficit to make up on Arsenal in fourth – with the Gunners also holding a game in hand.