Maloney, who scored a spectacular late winner against Macedonia last month, has missed Wigan's last four matches with a back injury and is not in Gordon Strachan's squad for the October 15 clash at Hampden.
Celtic winger James Forrest, who has missed recent action because of sciatica and a virus, is also absent for fitness reasons despite coming off the bench during his team's Champions League defeat by Barcelona on Tuesday night.
Scotland manager Gordon Strachan has otherwise picked a largely familiar squad with the suspended Steven Whittaker the only other significant omission following last month's double header against Belgium and Macedonia.
Derby midfielder Craig Bryson, Rangers left-back Lee Wallace and Birmingham winger Chris Burke retain their places after being handed late call-ups last month.
Hull pair Allan McGregor and George Boyd are in the squad following injury along with West Brom midfielders Graham Dorrans and James Morrison. St Mirren goalkeeper Craig Samson and Nottingham Forest forward Jamie Mackie drop out.
Scotland squad to face Croatia in a World Cup qualifier on October 15:
Gilks (Blackpool), Marshall (Cardiff), McGregor (Hull); Greer (Brighton), Hanley (Blackburn) Hutton (Aston Villa), Martin (Norwich), Mulgrew (Celtic), Wallace (Rangers); Adam (Stoke), Anya (Watford), Bannan (Crystal Palace), Brown (Celtic), Bryson (Derby) Burke (Birmingham), Dorrans, Morrison (both West Brom), McArthur (Wigan), Snodgrass (Norwich); Boyd (Hull), Griffiths (Wolves), McCormack (Leeds), Naismith (Everton), Rhodes (Blackburn).