Coach Ognjen Vukojevic and Croatian defender, Domagoj Vida, published a ‘glory to Ukraine’ video on to social media following the win.
According to the MailOnline, their actions were criticised by Russian politicians and led to a warning from FIFA’s disciplinary committee.
And now Vukojevic has been stripped of his accreditation and relieved of his duties.
Relations between Ukraine and World Cup hosts Russia remained undesirable after Russia’s 2014 annexation of the Crimean peninsula and its backing for a pro-Russian uprising in the east of the country.
Croatia’s Football Federation (HNS) said it has revoked Vukojevic’s team accreditation at the World Cup and relieved him of his duties as an observer for the Croatia squad.
In their full statement, HNS said: “Vukojevi? published a controversial video on social media after the match between Croatia and Russia in the quarter-final of the FIFA World Cup. The FIFA have opened a disciplinary procedure on the matter.
“The Croatian Football Federation (HNS) has decided to revoke Vukojevi?’s team accreditation at the FIFA World Cup and to relieve him of his duties as an observer for the Croatian national team.
“HNS hereby apologizes to the Russian public for the actions of a member of the Croatian delegation.
“Ognjen Vukojevi? and Domagoj Vida likewise apologize for their statements, which were in no way intended to have political connotations, yet which unfortunately left room for such interpretations.”
FIFA issued a formal warning to Vukojevic regarding his behaviour and the former midfielder reacted to his dismissal by telling Russian newspaper Sport Express: “There’s no politics in football. It’s a joke for my friends from Dynamo Kiev. I love Russians and I love Ukrainians.”
Both Vukojevic and the 29-year-old Vida previously played for Ukrainian club Dynamo Kiev.
Saturday’s match against Russia saw the two teams battle into extra time with Vida scoring at 100 minutes with the added bonus of a salute from the nation’s president, Kolinda Grabar-Kitarovi?.
Seconds after he was handed a yellow card when he took his top off during his celebrations.
The game went on to penalties and Croatia scraped through to the semi-finals when they won 4-3.
They will play England in Moscow on Wednesday at 7pm.