Play was suspended as the Croatia players appealed for calm in the closing stages of the match when they were 2-1 ahead.
The Czechs, who had pulled a goal back after falling 2-0 behind, grabbed a last-gasp equaliser and Cacic was in no doubt that the trouble had deprived his distracted team of victory.
“We suffered a complete meltdown on the pitch because of a handful of irresponsible individuals and if the game had gone on for any longer, we might have lost it,” he said.
The Croatians, who would have reached the last 16 with a match to spare with a win over the Czechs, play holders Spain in Bordeaux in their final Group D match on Tuesday.