The Croatian football association stripped Vukojevic of his role as an assistant in the team's delegation in Russia and FIFA fined him $15,000 over an Instagram video featuring him and Croatia defender Domagoj Vida, who shouted "Glory to Ukraine!"
Vukojevic posted the video after Croatia beat Russia on penalties in the quarter-finals.
Vida escaped with a warning from FIFA and is expected to be part of Croatia's team to face England in the World Cup semi-final on Wednesday.
He used to play for Ukrainian club Dynamo Kiev and Vukojevic also played for Dynamo and now works for them as a scout.
FIFA said Tuesday it was "looking into" another video of Vida apparently making political statements, including "Glory to Ukraine".
The phrase was a famous rallying cry of the former Soviet republic's pro-EU revolution that toppled a Russian-backed president in 2014.
The EU-backed uprising was followed by Russia's annexation of Ukraine's Crimea peninsula and the outbreak of a Kremlin-backed separatist conflict in eastern Ukraine that has claimed more than 10,000 lives.
While many in Ukraine compared the phrase to neutral slogans such as "Vive la France", some say it has distinct anti-Kremlin connotations.
The action against Vukojevic sparked Ukrainian anger towards FIFA as well as a wave of support for Vida and Vukojevic.
"We decided to compensate Vukojevic from our personal funds for the fine that he will have to pay," Ukraine football federation chief Andriy Pavelko wrote on Facebook.
"In addition, we are ready to consider the options for cooperation of FFU with such a high-class specialist," Pavelko said, in a post that included a picture of himself in a Croatia jersey.
'Offended millions of fans'
Ukraine's foreign ministry slammed FIFA's "unprofessional actions".
"Not only did they take the wrong decision about the Croatia players, they also offended millions of fans from Ukraine, Croatia and other countries," Oleksiy Makeev, the foreign ministry's political director, told AFP.
He slammed FIFA for turning a blind eye to Russia's involvement in the Ukraine and Syria conflicts.
Around 160,000 angry internet users, mainly Ukrainians, gave the FIFA official Facebook page a one-star review and wrote comments such as "Glory to Ukraine!" or "Shame to FIFA!"
On Tuesday, a small protest took place in front of the Croatian embassy in Ukraine's capital Kiev in a show of support, AFP journalists saw.
A group of around 15 people chanted "Glory to Ukraine" and held Croatian flags and placards praising Vukojevic and Vida.
On Sunday, Ukraine's football governing body also sent a letter to FIFA chief Gianni Infantino saying that "Glory to Ukraine!... is not a discriminatory or far-right sign or symbol".
It "should not be interpreted as an act of aggression or provocation," the body said.
In the video, Vukojevic also said: "This victory is for Dynamo (Kiev) and for Ukraine! Croatia onwards!"