U.S. District Judge Amul Thapar in Knoxville said he wanted the sentence to send a signal that others need to work for change within the bounds of the law.
The three activists have been in custody since May, when a federal jury convicted them of damaging the Y-12 National Security Complex in Oak Ridge, and could have received up to 20 years for the crime.
Rice, a member of the Sisters of the Holy Child Jesus, broke into the Tennessee facility with Greg Boertje-Obed, 58, and Michael Walli, 64. The three used wire cutters to slice through multiple security fences.
Boerjte-Obed and Walli were each sentenced to 62 months. In addition to their sentences, the three will receive three years of supervised probation after their release.
Unexpected snow delayed the original sentencing, which had been scheduled for Jan. 28. Then a federal judge ordered that the three pay nearly $53,000 in damages to cover facility repairs.
The Tennessee facility, also known as the "Fort Knox of Uranium," was used in the development of the atomic bomb that was dropped on Hiroshima in the summer of 1945.
The protesters belong to Transform Now Plowshares, an interfaith group that advocates nonviolent resistance to nuclear weapons.
Once inside the fence, the three spray-painted messages, including "the fruit of justice is peace," and splattered blood on one of the buildings.
The three also beat hammers against the walls of the facility in reference to the Bible's Isaiah 2:4, "They shall beat swords into plowshares and their spears into pruning hooks."
When approached by a guard, the three lit candles, sang songs and offered to break bread.
Defense attorneys stressed that the three were "completely nonviolent" and said that should be taken into account during sentencing.
But Assistant U.S. Attorney Jeff Theodore argued that even though he has great respect for their dedication to their cause, the three should be sentenced according to federal guidelines because "they are not above the law."