Croatia self-imploded on and off the pitch as a performance Ivan Rakitic labelled a thing of beauty was overshadowed by the ugliness that has become a depressing feature of this European Championship. Ante Cacic’s players were hugely impressive for the 62 minutes that Luka Modric graced the pitch. A few of their supporters were appalling for a brief period and the Czech Republic capitalised on the distraction to claim a point they scarcely deserved.

Rakitic appeared to have rewarded Croatia’s dominance with three points when he clipped a fine finish over Petr Cech, doubling their advantage following Ivan Perisic’s first-half strike. Moments later Modric, the game’s creative heartbeat, was withdrawn as a precaution against a groin problem. Even when Czech substitute Milan Skoda scored with 14 minutes remaining there appeared little challenge to Croatia’s authority or poise.

But then a bright red flare landed on the pitch to the left of Cech’s goal. Then another, then another, until at least 15 flares thrown by Croatia supporters marked the signal for a small group to attack their compatriots. One steward fell when a flare exploded. The referee, Mark Clattenburg, called a halt to proceedings for several minutes while a Croatian PA announcer pleaded with their fans to “leave the stadium and don’t embarrass our country”. A threat to abandon the game was also made.

Croatia’s captain, Darijo Srna, led player appeals to the supporters to halt the violence. Srna had displayed immense character and national pride to lead his country days after attending the funeral of his father in Metkovic. Tears streamed from his face during the national anthem. “My father’s last wish was that I play here, as this is my last competition for Croatia,” the 34-year-old said. “He was at his happiest when I played for Croatia.”

Would those Cacic described as “sporting terrorists” heed their broken captain’s instruction? Of course not. They rampaged on and Croatia – their players distracted by the knowledge their families and friends were in the same section of the stadium – lost their composure. Domagoj Vida’s needless handball in the 94th minute enabled another Czech substitute, Tomas Necid, to equalise with an emphatic penalty. A depressing result for Croatia but a more depressing episode could have damaging repercussions for one of the strongest sides at the tournament.

Rakitic, the Barcelona midfielder, said: “It would be stupid to find an excuse after the match was stopped and I don’t want to do it, but it’s clear, it’s happened before. After the match stopped they scored and it does have a connection with everything else. You all saw what happened and it’s not easy after such a beautiful performance.

“I think most moral supporters are supporting this team, real supporters, and these 10 or so individuals can make all these problems. The Croatian FA, especially Davor Suker [the president] are fighting against this. We just have to say sorry to Uefa, to the Czech Republic, all people around the world following this tournament and who love football. We have to play our matches in a better atmosphere and I hope Uefa can understand this. In the next qualifiers we have to play in empty stands and stadiums because of all these stupid supporters.”

His anger was perfectly understandable and justifiable. Croatia were too strong, too quick and, in Modric, too incisive with their passing for the Czech Republic when the game was just a game. The question was whether they could find the cutting edge to match as several promising moves, through balls and dangerous free-kicks passed without an end product.

The pressure on Cech’s goal was unrelenting in the first half. Those in front of the Arsenal goalkeeper lacked belief or quality in possession to stem the tide. The veteran keeper was exposed once again when Milan Badelj dispossessed Jaroslav Plasil in central midfield and the ball broke to Perisic on the left. The Internazionale midfielder advanced into the area, the central defender Tomas Sivok backed off, and Perisic accepted the invitation to drive a low finish into the far corner of the goal. Perisic immediately pointed to Srna as the celebrations commenced before running to the technical area to embrace Marjan Mrmic, the Croatia goalkeeping coach who also lost his father this week.

Despite a more determined start to the second half the Czechs gifted Croatia a seemingly comfortable lead when Plasil was again caught in possession. Marcelo Brozovic was at his heels this time and, with the Czech defence parting before him while playing a woeful offside trap, threaded a simple pass through to Rakitic who advanced on goal before beating Cech with a nonchalant chip. Vrba responded by bringing on Skoda and Josef Sural, to jeers from the Czech supporters, but their impact was immense. Tomas Rosicky had been on the periphery of the contest yet transformed the mood with an exquisite cross that invited Skoda to soar above Vedran Corluka and steer a header beyond the tame defence of goalkeeper Danijel Subasic.

In stoppage time Clattenburg penalised Vida for deliberate handball in the penalty area as he challenged Sivok in the air. Necid drilled a nerveless penalty down the centre of Subasic’s goal as Croatia spoiled their performance in more ways than one.

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