With Croatia 2-1 up and with one foot in the last 16, referee Mark Clattenberg briefly halted play late in the game when flares thrown by Croatian fans landed on the pitch in Saint-Etienne.
When the match resumed, Croatia defender Domagoj Vida was penalised for handball and Tomas Necid drilled home the resulting penalty, deep in added time, to claim their first point in Group D.
European football’s governing body UEFA are poised to impose further sanctions on the Croatian Football Federation for the crowd trouble.
“These people are terrorists, they are not fans,” fumed Croatia coach Ante Cacic.
“95 percent of our supporters are ashamed in front of Europe, the players are very sad that after playing a beautiful match this happens.”
Croatia were stripped of one point in qualifying, forced to play two home matches behind closed doors and fined 100,000 euros ($112,000) by UEFA after a swastika was painted on the field before a match against Italy in June 2015 in Split.
A member of the ground staff at the Stade Geoffrey Guichard appeared to have been hit by a flare.
Punches were also seen being thrown on the terraces amongst Croatian fans in the chaos of the closing stages.
“I must say the pause due to their fans helped us,” said Czech Republic goalkeeper Petr Cech.
“They were in control at that time and they suddenly lost rhythm and we could capitalise on that. We regained composure and although they had some counter-attacks (before the pause), from that moment on they didn’t have anything.”
Croatia were cruising towards the last 16 after their two Ivans — Rakitic and Perisic — netted either side of the break.
Having beaten Turkey 1-0 in their opener at the European championship finals, Croatia appeared to have their second win in the bag.
But Czech replacement Milan Skoda pulled one back before fellow replacement Necid’s dramatic spot-kick.
Captain Darijo Srna took his place at right-back after returning from father’s funeral back in Croatia and shed a few tears during his country’s anthem in an emotional start to a tense encounter.
Striker Mario Mandzukic had a field day playing in front of Real Madrid’s Luka Modric, whose stunning volley earned all three points against Turkey, while Barcelona’s Rakitic capped a good display with his goal.
Having threatened earlier in the half, Croatia took the lead on 37 minutes after a mistake in the Czech midfield.
Jaroslav Plasil lost the ball and Croatia’s Milan Badelj snapped up possession on the halfway line to quickly feed Perisic.
The 27-year-old Inter Milan winger attacked the Czech area, wrong-footed defender Thomas Sivok and curled his shot past Cech on 37 minutes.
It was 1-0 at the break and Croatia doubled their lead when Brozovic fed Rakitic inside the area.
The attacking midfielder’s classy chip gave Cech no chance as it hit the net on 59 minutes.
Only a fine Cech save prevented a third before Mandzukic fired over shortly after and Modric went off on 62 minutes struggling with an injury with his side in control.
But Skoda proved there was still some life in the Czech engine when he managed to put some power into his header from Tomas Rosicky’s cross on 76 minutes.
The flares then began to fall, briefly halting the game and leading to nine minutes of extra time, which gave the Czechs the chance to equalise against a distracted Croatian defence.
Croatia now face defending European champions Spain in Bordeaux on Tuesday.
The fightback gives the Czech Republic a realistic chance of making the knock-out stages with victory in their final game against Turkey in Lens, also next Tuesday.