Fans in the Croatia section of Saint-Etienne's Stade Geoffroy-Guichard threw flares onto the pitch before fighting among themselves, leading to referee Mark Clattenburg to bring a halt to proceedings of the Group D fixture for around five minutes.
Vrba's side were 2-1 down at the time, but went on to secure a point that keeps their hopes of reaching the last 16 alive thanks to a nerveless injury-time penalty from Tomas Necid.
Croatia boss Ante Cacic slammed the supporters at the centre of the trouble - who are believed to have been demonstrating against the Croatian Football Federation - after the game, calling them "sports terrorists", while UEFA confirmed they will investigate the issue.
And Vrba was keen to stress that he expects the governing body to hand down the correct sanction.
"Of course it makes me sad, but this is a UEFA thing. It doesn't concern us, UEFA will decide," Vrba told his post-match media conference.
"I prefer when the fans support their team, as they did until the 80th minute. The Croatian fans were great up until that moment. Please don't be angry with me, but it doesn't concern me at all."
Czech Republic face Turkey in their final Group D game on Tuesday, knowing that a win could see them through to the first knockout round.
However, Vrba may have to do without his captain Tomas Rosicky after the veteran midfielder picked up a thigh problem.
"We'll know tomorrow," the coach replied when asked about the extent of Rosicky's injury.
"He's got problems with his thigh muscle. The question is if this is because he gave everything on the pitch, whether it's a cramp or a more serious problem."