Fears over Luka Modric's fitness were put to one side by Croatia coach Ante Cacic, who insisted he had withdrawn the talisman against Czech Republic as a precaution to preserve his "most important player".
Cacic's side were cruising at 2-0 up in Saint-Etienne when the Real Madrid midfielder was substituted just past the hour mark.
It proved to be detrimental for Croatia at Stade Geoffroy-Guichard, where crowd trouble interrupted the game, as Czech Republic came from behind to draw 2-2.
Cacic's side - now set to face a UEFA investigation for the actions of their supporters, who thew several flares onto the pitch - are still in prime position to qualify from Group D.
They face holders Spain in Bordeaux on Tuesday but it remains to be seen if Modric will be risked.
"Luka Modric is just tired and had a stretched muscle problem," Cacic told a press conference. "Luka is the most important player for us."
Croatia had dominated the match and looked set to win with ease before Milan Skoda pulled one back, Tomas Necid then equalising from the penalty spot late on after troubling scenes of disorder among the Croatian fans, who threw a succession of red firecrackers onto the pitch before fighting among themselves.
"We were the much better team," Cacic said. "We had good possession. We tried everything. Our biggest problem today was with Luka Modric. We were not concentrated that much when he left the pitch."