The Wolves centre-back was sent home from the squad as a precaution but is expected to be okay for Wednesday night's final Group Nine game with Holland.
Berra's absence leaves Scotland boss George Burley with just three centre-halves to choose from against Macedonia, and it appears certain Celtic captain Stephen McManus will start his first game of the season alongside veteran Rangers skipper David Weir.
Gary and Steven Caldwell are ruled out through suspension and injury, respectively, while Darren Barr has won only one cap.
McManus has been sidelined since picking up a knee injury last season and has yet to play under new Celtic boss Tony Mowbray.
The 26-year-old played in a reserve-team game for the Hoops last week and has taken a full part in training with the national squad in the last few days.
But his selection would be a gamble for Burley, who cannot afford anything other than victory on Saturday if Scotland are to keep their slim hopes of reaching the World Cup play-offs alive.
As well as Steven Caldwell, Burley has already lost Kilmarnock striker Kevin Kyle to injury, while third-choice goalkeeper Neil Alexander will miss the Macedonia game after picking up a knock in training.
Aberdeen's Jamie Langfield has been drafted in as cover, and Birmingham striker Garry O'Connor was this week called up to replace Kyle.