"We are very pleased with this development and hope that it will have a positive impact on the court case in Moscow," Judah Schroeder, a spokesman for the Jehovah's Witnesses, said by telephone from the United States.
He said the group had been re-registered under the name "Administrative Center for Jehovah's Witnesses in Russia."
He added that the right to use the word "Russia" in its official name was given only to religious organizations that had existed in the country for more than 50 years.
All religious organizations in Russia have to be re-registered under the 1997 law "On freedom of conscience and religious organizations," which has been criticized by human rights groups and by the United States as discriminatory.
That law also gives the courts the right to disband groups they find guilty of inciting hatred or intolerant behavior.
Moscow prosecutors began their attempt to close down the Jehovah's Witnesses in the Russian capital after accusing the group of breaking up families and preaching intolerance.
The Jehovah's Witnesses say the prosecutors have failed to produce any evidence to back up their claims and say the case recalls Soviet-era efforts to control all religious activity.
The group says it has existed in Russia for more than a century and claims about 250,000 members nationwide.
In March a judge overseeing the court case ruled that a panel of experts should decide whether or not to uphold the prosecutor's claims and ban the Jehovah's Witnesses.
The Jehovah's Witnesses issued a statement welcoming the Justice Ministry's decision to re-register them.
Vasily Kalin, director of the Witnesses' Administrative Center in St Petersburg, said the move underscored Russia's shift towards democracy and respect for human rights.
"After living through persecution for my religious beliefs under the Communist regime, I am happy to see that the freedom to practice my religion openly that was granted in 1991 will continue," Kalin said.
Human rights groups also hailed the ministry's move.
"The Russian Federation's decision to re-register the Jehovah's Witnesses is the right decision. We hope that local officials in Moscow will follow suit," said Lyudmila Alekseyeva, president of the International Helsinki Federation.