Abid Naseer and Ahmad Faraz Khan, both 23, were among 12 men, mostly students, arrested in high-profile raids across northwest England in April 2009.
Police and the security services said at the time the men were part of a major plot. But there was not enough evidence to charge them and they were ordered to be deported.
The Special Immigration Appeals Commission (SIAC), which deals with such cases, said the two men should not be sent back to Pakistan because of the risk they would be mistreated there.
However, it said it believed Naseer was a security threat and ideally should be removed from Britain. It said Faraz Khan could "safely be taken to have been willing to participate" in Naseer's plans, the Press Association reported.
"We are satisfied that Naseer was an Al-Qaeda operative who posed and still poses a serious threat to the national security of the UK and that... it is conducive to the public good that he should be deported," the commission said in a written ruling.
It said the government believed the men were part of a plot to carry out a "mass casualty" attack in April last year in northwest England.
However, no explosives were found, and the government's case was based around emails exchanged between Naseer and a Pakistan account believed to be registered to an Al-Qaeda operative.
A third man detained in the raids in Manchester and Liverpool, Shoaib Khan, 31, who already is back in Pakistan, won his appeal against exclusion from Britain.
Two other men back in Pakistan, Abdul Wahab Khan, 27, and Tariq Ur Rehman, 38, had appeals against exclusion rejected.
Several hundred officers took part in the raids, which had to be hurriedly brought forward after Britain's most senior counter-terrorism officer was photographed openly carrying a secret document detailing plans for the arrests.
The government said it was disappointed at the ruling but would not appeal.
Britain has demanded Pakistan do more to combat terrorism.
Most terrorist plots in Britain since Sept. 11, 2001 have had links to Pakistan, including suicide bombings in July 2005 which killed 52 people on London's underground and bus network.
