The centre-back was investigated by world football's governing body over comments he made in a social media video after Croatia's quarter-final victory over hosts Russia.
The phrase has been used by Ukrainian anti-Russian nationalists, with Vukojevic adding: "This victory is for Dynamo and Ukraine."
FIFA's disciplinary code prohibits "political slogans in any form" with "anyone who provokes the general public during a match" facing a two-game ban.
Earlier in the tournament Switzerland players including Xherdan Shaqiri were fined but not banned for making hand gestures resembling an eagle, a symbol of Albania, against Serbia earlier in the World Cup.
And now have FIFA confirmed that Vida will not be punished over the incident.
"We can confirm that FIFA's disciplinary committee has sent a warning to the player Domagoj Vida due to his video statement following the 2018 World Cup match between Russia and Croatia," said a FIFA statement.
Vida, an extra-time goalscorer in Croatia's defeat of Russia on penalties, will now be available as his side aim to reach the World Cup final for the first time.