The Croatian federation (HNS) was charged with "crowd disturbances, use of fireworks, throwing of missiles and racist behaviour", European soccer's ruling body said in a statement.
UEFA said the ticket restriction, under which supporters identified by the HNS and Croatian authorities as hooligans would be banned from buying tickets, will be applied if any more incidents occur.
"This sanction is deferred under a probationary period until the end of the tournament," said the UEFA statement.
The crowd trouble occurred during their Group D match on Friday against the Czech Republic in St Etienne, which was held up for several minutes after Croatian fans threw flares onto the pitch and began fighting among themselves.
A dozen flares plus other objects landed on the pitch near to riot police, who had been deployed in front of the section housing Croatia's supporters.
The trouble broke out in the dying minutes of a game that Croatia were leading 2-1. The final score was 2-2.
The Croatian FA, sanctioned three times in the qualifying competition, was already facing a disciplinary hearing on Tuesday after fans threw flares and ran onto the pitch during the team's opening match at the finals against Turkey in Paris.
(Reporting by Julien Pretot; Editing by Neil Robinson and Ken Ferris)
