The disciplinary committee of Russian soccer's governing body could have docked the club points or issued a fine, but decided to punish the Zenit fans.
The banner, which insulted the memory of one of the country's greatest ever players, was displayed by Zenit fans during Sunday's Premier League match against Dynamo Moscow and read "Your Yashin snuffed it, and Dynamo will snuff it."
The press service for Zenit said that the club regrets the incident and accepts the penalty.
"Zenit accepts the decision of the Russian Football Union's disciplinary committee on holding a home match without spectators. We regret that a nasty escapade of a small group of people resulted in depriving 22,000 Zenit fans of the right to visit the stadium, and that because of this the team will be left without supporters," the press service said.
This season Zenit has only one game left in Russia's Premier League, away against Spartak Moscow on Saturday, so the penalty will come into force for Zenit's first home match of the 2009 season.
Lev Yashin (1929-1990) is the only goalkeeper ever to have won the European Player of the Year Award. He spent his whole career, from 1949 to 1971, at Dynamo. The keeper, who wore all black when defending his goal, won world fame with his breathtaking performances in the 1966 World Cup in England, as the Soviet Union reached the semifinals.
"The Black Spider," as he was known throughout the world, was credited with revolutionizing the art of keeping goal with his willingness to come off his line to deal with opposing attacks. He was voted the best goalkeeper ever by the International Federation of Football History & Statistics.
In 1994, FIFA established the Lev Yashin award for the best goalkeeper at the World Cup. Yashin's FIFA testimonial game at Luzhniki stadium in Moscow was attended by 100,000 fans, who saw appearances by soccer legends such as Pele, Eusebio and Franz Beckenbauer. There is also bronze monument to Yashin at Dynamo's home ground.
Russian soccer fans have a long tradition of bringing banners to matches. Before last year's Russia vs England game in Moscow, "the largest banner in the world," depicting a bear, was unfurled before kick-off.
Banners are frequently of a less savory nature, however. In 2006, a swastika was displayed by Spartak Moscow fans at an away game in Yaroslavl, 250 km (155 miles) northeast of Moscow.
