The incident occurred on April 5 in the capital's Luzhniki Stadium during Spartak Moscow's match against Spartak Nalchik.
The head of the Football Union's disciplinary committee said the ruling on the 500,000-ruble fine took into account the circumstances of the incident, and the text on the banner.
The one-word message consisted of seven Cyrillic letters held up by a group of fans in the stadium's Sector C. Spartak Moscow won the match 2-0.
The banner "consisted of an obscenity, with elements of an insulting nature," Vladimir Katkov said.
"The identity of those who were holding the banner has not yet been established, but work on this is ongoing," he said.
The complaint over the banner was lodged by the general director of Spartak Nalchik, Vladimir Balov, who said the message "offended the honor and integrity of the club, our fans, and the population of the Kabardino-Balkaria republic."
The public use of swearwords, or "mat" in Russian, is prohibited under the country's legal code and punishable by a fine or a custodial sentence of up to 15 days. However, the law is rarely enforced.
In another recent banner incident, Zenit St. Petersburg were forced to play their first home match of the 2009 season behind closed doors after the club's fans unfurled a banner insulting the memory of Lev Yashin, one of the country's greatest players, during a game against Dynamo Moscow late last year.
The banner read "Your Yashin snuffed it, and Dynamo will snuff it."
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 Moscow.
