A panel of five judges ruled there were no grounds to reconsider a decision that the hate cleric would not face torture if returned to Jordan, sources said.
The decision was a narrow escape for Theresa May, Home Secretary, after the court decided the application was submitted within time.
The firebrand will remain in the country for up to a year because he will now resume a separate legal challenge against assurances that he will face a fair trial.
Qatada was arrested and returned to custody last month after the Home Secretary resumed his deportation.