Television pictures showed the Palestinian-born preacher dressed in a white robe and boarding the the privately chartered aircraft at the RAF Northolt airbase in west London before it lifted into the sky at 0146 GMT.
British Home Secretary Theresa May confirmed that the 53-year-old, once dubbed Osama bin Laden's right-hand man in Europe by a Spanish judge, had left the country.
"Abu Qatada was deported today to his home country of Jordan to face terrorism charges," May said in a statement.
Britain has been taking legal action against Abu Qatada since 2001 but only formally launched extradition proceedings against him in 2005.
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Abu Qatada had earlier left high security Belmarsh jail in southeast London in a blue armoured police van flanked by two saloon cars and a Range Rover, which whisked him to the airfield.
Britain is deporting the Palestinian-born cleric after the two governments last month formally approved a treaty guaranteeing that evidence obtained by torture would not be used against him in any retrial.
In 2000, he was sentenced to 15 years for plotting to carry out terror attacks on tourists during the millennium celebrations in Jordan.
Under Jordanian law, Abu Qatada faces retrial for the offences on his return, because the original convictions were made in absentia.