The Hannover forward, who will also miss Austria's game in Serbia on Sunday, has been replaced by Sturm Graz striker Deni Alar
Harnik is the team's most-capped player, with 14 goals in 61 matches.
Alar is the leading top-scorer for Austrian league leaders Graz, with nine goals in as many games.
Austria winger Martin Harnik will miss Thursday's World Cup qualifier against Wales in Vienna because of a calf injury.