The Universal Church of the Kingdom of God was banned last month after a series of riots.
Members of the UCKG are now free to meet until the legal case is settled.
The decision temporarily overturns a government decision to de-register the sect and deport its two Brazilian pastors - who can now stay on.
They had earlier been given seven days to leave the country.
The BBC's Musonda Chibamba in Lusaka said applause and jubilation greeted the ruling.
The church took the government to court shortly after the ban was imposed, saying they had not been allowed to present their side of the story and that they had been the victims of public hatred and persecution.
Several church buildings, including a new cathedral, were damaged in riots after word went round that the church had detained two men against their will for alleged satanic rituals.
In 1998, the UCKG was shut down for what was termed "unchristian practices", but the church took the matter to the Supreme Court, which nullified the ban.