FIFA announced the sanctions Saturday but did not order full or partial stadium closures for the playoff matches starting next week.
FIFA fined the Croatia Football Federation 35,000 Swiss francs ($38,000) for incidents during its 2-1 loss against Belgium in Zagreb on Oct. 11.
"Croatian supporters made far-right salutes which were used during World War II by the fascist Ustase movement," fan monitoring group Fare reported to FIFA.
FIFA fined the Greek federation 30,000 Swiss francs ($32,500) following reports of far-right banners displayed when Greece beat Slovakia 1-0 in Athens on Oct. 11.
In the playoffs, Croatia hosts Iceland in the second leg on Nov. 19, and Greece hosts Romania in the first leg on Friday.
In September, Ukraine was found guilty by FIFA of racist behaviour by fans at a qualifying match, but has escaped a closed-stadium order when it hosts France on Friday in Kyiv.
FIFA deferred the punishment while it considers Ukraine's appeal after fans made monkey noises at the team's Brazil-born player Edmar during a win against San Marino in September in Lviv. FIFA also banned the Lviv stadium from hosting qualifying matches for the 2018 World Cup.
In other sanctions on Saturday, the Croatia federation was also fined 15,000 Swiss francs ($16,300) for "crowd disturbance among visiting spectators" during a World Cup qualifier in Scotland on Oct. 15. The Scottish FA, which was responsible for security at the match in Glasgow, was also fined 10,000 Swiss francs ($10,850).
Romania's federation was fined 10,000 Swiss francs ($10,850) for crowd disturbances at a home qualifier in Bucharest against Estonia last month.