The Christian sect's administrative centre near St Petersburg and 395 local organisations were added to the list by the justice ministry on Thursday.
Believers can now be charged for proselytising or gathering together.
In April, Russia's Supreme Court decided in favour of the justice ministry's characterisation of members of the Jehovah's Witnesses as posing "a threat to the rights of the citizens, public order and public security."
The denomination's properties, known as Kingdom Halls, will also be seized by the state.
The Jehovah's Witnesses are expected to appeal the ban at the European Court of Human Rights.
The British Government previously said it was "alarmed" by the ban and launched an appeal for Vladimir Putin to uphold religious freedom in Russia.
Jehovah's Witnesses, who are known for their door-to-door preaching and distribution of literature, reject some of mainstream Christianity's core beliefs.
The US-based group, which has more than 8.3 million adherents around the world, has generated controversy for its stances including the rejection of blood transfusion and opposition to military service.