Radical cleric Abu Qatada is being held in a high security jail near the Jordanian capital Amman, after being deported from the UK.
His plane left RAF Northolt at 02:46 BST for his home country, where he appeared in court to be charged with terror offences, which he denies.
Prime Minister David Cameron said he was "delighted" at his removal.
Abu Qatada was first arrested in the UK over alleged terror connections in 2001 and has fought deportation since 2005.
The Palestinian-Jordanian cleric's deportation was finally able to proceed after the UK and Jordan signed a treaty agreeing that evidence obtained through torture would not be used against him.
Home Secretary Theresa May said she was glad that the government's determination to remove him had been "vindicated".
"This dangerous man has now been removed from our shores to face the courts in his own country," she said.
She added that she wanted to streamline such deportation processes in future.
"I am also clear that we need to make sense of our human rights laws and remove the many layers of appeals available to foreign nationals we want to deport.
"We are taking steps - including through the new Immigration Bill - to put this right."
'Nothing off table'
Changes to the bill would affect cases like Abu Qatada's, she said, and also cases in which people facing deportation claim they have a right to respect for their private and family life in the UK, as set out in article eight of the European Convention on Human Rights.
Mrs May said she hoped to reform the convention, and would not rule out the possibility of the UK withdrawing from it altogether.
"Nothing is off the table," she said.
"We're working on that at the moment," the home secretary told the BBC, adding that the Conservative manifesto for the 2015 general election would "set out clearly what we would do in relation to these issues".
Abu Qatada was accompanied on the flight of around five hours by six people from Jordan, comprising three security officials, a psychologist, a medical examiner and his Jordanian lawyer, the BBC understands.
The 53-year-old had been held at Belmarsh prison in south-east London, from where a convoy of three police vehicles left at midnight.
After arriving at Jordan's Marka military airport he was driven in a green SUV, escorted by a 12-car convoy, to the sealed off state security court in Amman.
Military prosecutors charged him with conspiracy to carry out terrorist acts - relating to a plot to bomb American and Israeli tourists during Jordan's millennium celebrations.
The cleric was remanded in custody for 15 days and taken to eastern Jordan's Muwaqqar prison, a judicial official said.
After the hearing his lawyer Tayseer Diab said: "The attorney general interrogated him today, and he directed a series of accusations towards him - he accused him of conspiracy to take part in terrorist acts.
"My client denied all the allegations, and he asserts that his return to Jordan was out of his own free will, in order to be with his family. The procedure was carried out well, and he received good treatment."
Speaking outside the court, Abu Qatada's father Mahmoud said: "His spirits are high and the officials are good people - they might allow him to obtain bail after a few days."
BBC home affairs correspondent Dominic Casciani said Home Office officials were "incredibly relieved" after "one of the most tense weeks in the department's recent history".
"They were so concerned about the possibility that the cleric could change his mind at the last minute that they were leaving nothing to chance."
Speaking on BBC Breakfast, Mrs May said she had been provided with updates on the deportation throughout the night.
She said she had been "as frustrated as the public" about the estimated £1.7m cost and length of time it had taken to remove Abu Qatada, but that people would welcome the end result.
She said she did not have any concerns about the treatment of Abu Qatada in Jordan.
She said: "The treaty we've signed ensures that there are proper processes of exchange of evidence and will insure the treatment of Abu Qatada and others deported to Jordan."
Asked on Sky News whether Abu Qatada's wife and children would have the right to stay in the UK, Mrs May said they would have to decide what they want their future to be before the government gets involved.
Mr Cameron criticised a "caravan of lawyers" over the case, adding that it had "made my blood boil that this man who has no right to be in our country, who is a threat to our country and that it took so long and it was so difficult to deport him, but we've done it, he is back in Jordan that is excellent news."
Abu Qatada, whose real name is Omar Othman, was granted asylum in the UK in 1994 but the Security Service came to view him as a threat as his views hardened.
Richard Reid, the would-be mid-Atlantic shoe bomber, and Zacarias Moussaoui, both jailed for involvement in terrorism, are said to have sought religious advice from him.
The cleric's sermons were also found in a flat in the German city of Hamburg used by some of those involved in 9/11.
He vowed to fight the UK's 2005 decision to deport him to Jordan to face retrial over bomb plot allegations - setting in motion an eight-year legal battle.
The dispute continued until May this year, when the cleric accepted that his right to a fair trial there was protected by the new treaty between Jordan and the UK.
Labour's shadow home secretary Yvette Cooper welcomed the deportation and backed Mrs May's call for a more streamlined process in future.
She said: "The home secretary has been right to get further guarantees from Jordan and we should welcome the series of agreements from the Jordanian government too.
"We must ensure that delays like this do not last for so long in future and that the system is reformed to make it faster."
Keith Vaz, chairman of Parliament's Home Affairs Select Committee, questioned why the government had not started work on a treaty with Jordan at an earlier stage in the process.
"The home secretary's legal advisers will have questions to answer as to why they didn't conceive of this scheme earlier which would have prevented a cost to the taxpayer of £1.7m."