Last month the Special Immigration Appeals Commission (SIAC) ruled that Qatada should not be deported to Jordan where he was convicted of terror charges in his absence in 1999.
A panel of three judges found that there was a risk that evidence obtained using torture would be used against the controversial cleric in a re-trial.
Yesterday Theresa May submitted grounds for appeal to the Court of Appeal in a bid to overturn the SIAC's decision.
The only way the ruling can be challenged is if it is found there were legal problems with the commission's ruling.
The SIAC judges ruled on November 12 that evidence from Qatada's former co-defendants, Abu Hawsher and Al-Hamasher, said to have been obtained by torture, could be used against him in a re-trial.
"The Secretary of State has not satisfied us that, on a re-trial, there is no real risk that the impugned statements of Abu Hawsher and Al-Hamasher would be admitted probatively against the appellant," they said.
Mrs May immediately pledged to appeal and told the Commons that Jordan had given assurances about its legal processes. She said: "Qatada is a dangerous man, a suspected terrorist, who is accused of serious crimes in his home country of Jordan.
"The British Government has obtained from the Jordanian Government assurances not just in relation to the treatment of Qatada himself, but about the quality of the legal processes that would be followed throughout his trial. We will therefore seek leave to appeal."
Qatada was immediately granted bail following the ruling and released from HMP Long Lartin, returning to his family home in north London.
He is said to have wide and high-level support among extremists, and featured in hate sermons found on videos in the flat of one of the September 11 bombers.
The extremist has battled deportation for more than a decade.