Britain has signed special agreements with countries such as Jordan containing guarantees that deportees will be well treated.
The memoranda of understanding evade European human rights legislation which forbids member states from deporting people to countries where they could be tortured.
John Reid, the British home secretary, said in a statement: "We welcome the decision of the Special Immigration Appeals Commission that Abu Qatada presents a threat to our national security and can be deported.
"I am very pleased that the court has confirmed this, and that this procedure will enable us to meet our international obligations," he said.
"We are also pleased that the court has recognised the value of memoranda of understanding. It is our firm belief that these agreements strike the right balance between allowing us to deport individuals who threaten the security of this country and safeguarding the rights of these individuals on their return."
Abu Qatada has twice been convicted by Jordan in absentia on charges of involvement in terrorist plots.
Abu Qatada, who has been repeatedly linked to radical groups including the al-Qaeda network, is in detention awaiting the outcome of the case. He was not present in court.
The authorities say 18 videotapes of his sermons were found in an apartment in Germany used by three of the suicide hijackers who carried out the September 11 attacks on the US in 2001.