The Czechs battled back from two goals down to earn its first point of the tournament against a Croatia side which, after 60 minutes, appeared to be completely in control.
Ivan Perisic's first half strike and Ivan Rakitic's second half goal had seemingly wrapped up qualification to the last 16, before goals from Milan Skoda and Tomas Necid earned the Czech Republic an unlikely point.
However, in the game's dying embers, several flares were thrown onto the pitch by a section of Croatia supporters, resulting in one exploding next to a steward and fighting breaking out in the stands.
In Group D's late match, reigning champion Spain produced an imperious performance against Turkey, romping to a 3-0 win and securing safe passage to the knockout stage.
Croatia fans had been treated to a masterclass from Real Madrid's Luka Modric, as the midfielder orchestrated play from the middle of the pitch.
Having been utterly dominant for the opening half an hour, it was a questions of when, not if Croatia would take the lead.
It came as no surprise, then, that the deadlock was broken seven minutes later, Perisic latching onto a loose ball after Milan Badelj had won possession and firing a shot past Petr Cech.
With the Czech Republic chasing the game, defender Roman Hubnik attempted to pass the ball out from the back but inadvertently gifted possession to Marcelo Brozovic.
The Inter Milan midfielder fed the ball into Rakitic who coolly chipped the ball over the onrushing Cech.
With the game and qualification from Group D seemingly secured, Croatia opted to replace Modric who appeared to be struggling with an injury.
Czech Republic's Tomas Rosicky began to dictate play in the space afforded to him in Modric's absence and curled a delightful ball into the box with the outside of his boot, allowing Milan Skoda to power a header past Danijel Subasic.
Suddenly, Croatia was on the ropes.
With just three minutes left to play, a number of flares were thrown onto the corner of the pitch nearest Cech's goal. Play was stopped, resulting in 10 minutes additional time, to allow the stewards to remove them.
Play resumed with fan unrest still ongoing in the stands and the Czechs were awarded a penalty in the 93rd minute, after Domagoj Vida's blatant handball.
Tomas Necid stepped up and hammered the ball down the middle of the goal, sending those fans behind the goal into raptures and keeping the Czechs' hopes of qualification alive.
Spain, meanwhile, sent a message to its European rivals with a three-goal demolition of Turkey.
The 2012 winners stuttered to a labored 1-0 win against the Czech Republic in the opening round of fixtures but ran riot against a Turkey side devoid of idea and inspiration.
In truth, Spain could have scored any number and the final score doesn't quite reflect its utter dominance.
The tone of the game was set less than two minutes in, Barcelona defender Gerard Pique met Andres Iniesta's corner six yards out but his header bounced into the turf and over the crossbar.
Iniesta then started to dominate proceedings, feeding Nolito on the edge of the box just shy of the half hour mark. The Celta Vigo man swiveled sharply but curled his shot inches wide of Volkan Babacan's far post.
Less than five minutes later, Spain finally took the lead. Nolito's cross into the box was met by the head of Alvaro Morata, who deftly guided the ball into the far corner.
It took just three minutes for Spain to double the lead, a horrible error in the Turkish defense allowed Nolito to slide in and divert the ball past the helpless Babacan.
Turkey was helpless to withstand the wave after wave of red shirts led by Iniesta, and those present were privileged to witness one of the great recent midfield performances.
After 48 minutes, Spain became the first team to score three goals in a match at Euro 2016. Iniesta, yet again, at the heart of a wonderful team move, floating a ball into Jordi Alba who unselfishly squared the ball for Morata to tap in his second.
With victory secured, Spain took its foot off the gas and now look a solid bet to retain the European crown.
In Group D's final fixtures, the Czech Republic plays Turkey, while Croatia faces Spain.