The group, which says it has more than 170,000 followers in Russian Federation, has said it is "shocked" and will appeal against the decision in the European Court of Human Rights.
"They pose a threat to the rights of the citizens, public order and public security", justice ministry attorney Svetlana Borisova told the court.
"The Supreme Court has ruled to sustain the claim of Russia's Ministry of Justice and deem the "Administrative Center of Jehovah's Witnesses in Russia" organization extremist, eliminate it and ban its activity in Russian Federation".
Jehovah's Witnesses say the accusations are completely untrue.
Participants attend a hearing on the justice ministry request to ban the Jehovah's Witnesses at Russia's Supreme Court in Moscow on April 20, 2017. The Justice Ministry had asked the top court to outlaw the group on March 17, and had warned the group to end all its activity at its headquarters in St Petersburg.
A member of the Council of Europe and a party to the European Convention on Human Rights, Russia is obligated to protect freedom of religion and association.
The religious organization has expanded around the world and has about 8 million active followers.
"We will do everything possible", he said.
One pamphlet the ministry reportedly took issue with quoted the novelist Leo Tolstoy and described the beliefs of the Russian Orthodox Church as superstition and sorcery, according to the BBC.
The Jehovah's Witnesses group was founded in the United States in the 19th century.
He said he feared that members of the group could face prosecution if they continued to gather and study the Bible.
Its members are known for preaching on doorsteps, where they offer religious literature and attempt to convert people.
In January, the leader of a congregation in the town of Dzerzhinsk in the central Nizhny Novgorod region was fined for distributing materials that authorities deemed extremist, local media reported.
Jehovah's Witnesses pray at a regional congress at Traktar Stadium in Minsk, Belarus, July 25, 2015.