The Cardiff City striker's groin injury was assessed by the Scotland medical team after training on Friday, a session which the former Rangers and Celtic player did not complete.
The decision was then taken not to risk him, although manager Craig Levein is hoping he will be fit for the last Group I fixture against Spain in Alicante on Tuesday evening.
A statement on the Scottish Football Association website read: "Kenny Miller will not play against Liechtenstein.
"He will continue to be assessed ahead of Tuesday's match against Spain."
Rangers forward Steven Naismith, Brighton striker Craig Mackail-Smith and Blackburn's David Goodwillie are all in contention to replace Miller up front for Scotland.
Skipper Darren Fletcher could make a shock appearance for Scotland against Liechtenstein.
Levein had ruled Fletcher out with tonsilitis and the Manchester United player did not travel with the squad to their Switzerland base.
But the Scotland boss, speaking at the Scots' hotel in St Gallen, said: "Darren will arrive today and I have not 100 per cent ruled him out of tomorrow.
"He feels better. He will do something on his own today.
"I have to wait to see him and assess him. If the medical team gives him the thumbs up he will play, if not he is 100 per cent certain to be involved on Tuesday (against Spain)."
Midfielders Barry Robson (thigh) and Graham Dorrans (ankle) and defender Alan Hutton (knee) are all fit for Scotland.
Scotland (from): Marshall, McGregor, Bell, McManus, Whittaker, Hutton, Bardsley, Hanley, Wallace, Berra, G Caldwell, Adam, Bannan, Cowie, Dorrans, Fletcher, Forrest, Morrison, Robson, McArthur, Swanson, Naismith, Goodwillie, Mackail-Smith.
