"It's unpleasant, but this team has enough quality to handle the next two qualifiers well," Bilek told reporters after naming the Czech squad for the Scotland game and for another qualifier in Liechtenstein on 12 October.
Baros limped off the pitch with a torn thigh muscle after scoring a hat-trick against Buyuksehir in the Turkish league game on Sunday. Doctors said he might be out for two or three weeks.
Bilek, whose team lost 0-1 at home to Lithuania in the Group I opener, selected two newcomers - Sparta Prague's 18-year-old striker Vaclav Kadlec, and Milan Petrzela, a midfielder with Czech top-flight leaders Viktoria Pilsen.
Czech Republic squad
Goalkeepers: Petr Cech (Chelsea/ENG), Jan Lastuvka (Dnepropetrovsk/UKR), Tomas Grigar (Teplice)
Defenders: Roman Hubnik (Hertha/GER), Michal Kadlec (Leverkusen/GER), Zdenek Pospech (Copenhagen/DEN), Daniel Pudil (Genk/BEL), Marek Suchy (Spartak Moscow/RUS), Jan Rajnoch (Ankaragucu/TUR)
Midfielders: Tomas Hubschman (Shakhtar Donetsk/UKR), Mario Holek (Dnepropetrovsk/UKR), Jaroslav Plasil (Bordeaux/FRA), Tomas Rosicky (Arsenal/ENG), Jan Polak (Anderlecht/BEL), Jiri Stajner (Liberec), Milan Petrzela (Viktoria Pilsen)
Forwards: Tomas Necid (CSKA Moscow/RUS), Roman Bednar (West Bromwich/ENG), Lukas Magera (Timisoara/ROM), Vaclav Kadlec (Sparta Prague)