The State Department said that the officials in the western Siberian city of Surgut supervised interrogations on February 15 in which at least seven Jehovah's Witnesses were subjected to suffocation, electric shocks and severe beatings.
The State Department said that the two officials, Vladimir Petrovich Yermolayev and Stepan Vladimirovich Tkach, and their immediate families would be barred from entering the United States.
"Russia should end its unjust campaign against the Jehovah's Witnesses and immediately release the over 200 individuals it currently has imprisoned for exercising their freedom of religion or belief," State Department spokeswoman Morgan Ortagus said in a statement.
Russia outlawed the Jehovah's Witnesses in 2017, calling them an extremist organization.
Founded in the United States in the late 19th century, the non-violent movement has often faced problems for members' proselytization and refusal to salute state symbols such as flags.
A Russian court in May upheld a six-year jail sentence for a Danish Jehovah's Witness, in the first conviction since the 2017 ban.