The British resident, who was held at the US jail for more than four years, was set free from RAF Northolt.
He had arrived at the site at 1pm and was detained under border control rules which are part of the Terrorism Act 2000.
A statement from Scotland Yard said: "A man detained by officers from the MPS Counter Terrorism Command under Ports and Border Controls, contained within the Terrorism Act 2000, was released at 5.46pm today.
"The man had been detained at RAF Northolt shortly after 1300 hours today following his return from Guantanamo Bay."
Officers hoped to deal with his paperwork at the RAF base to avoid any need for him to be taken to the maximum security police station at Paddington Green in central London.
Mr Mohamed, 30, had been held at the controversial US military detention centre at Guantanamo Bay in Cuba since September 2004.
He said the worst moment of his captivity was when he realised his "torturers" were receiving questions and material from British intelligence agents.
He alleges he was tortured into falsely confessing to terrorist activities and claims MI5 officers were complicit in his abuse.
The Government requested his release and a team of British officials went to Guantanamo Bay recently to check he was well enough to travel back to the UK.
In a statement, Mr Mohamed said: "For myself, the very worst moment came when I realised in Morocco that the people who were torturing me were receiving questions and materials from British intelligence."
Ethiopian-born Mr Mohamed, who lived in London before his arrest in Pakistan in 2002, said he was neither physically nor mentally capable of facing the media immediately.
He is planning to spend the next few days with his family and legal team.
"I have been through an experience that I never thought to encounter in my darkest nightmares," he said.
He added that he never imagined he would be the victim of torture and said: "It is still difficult for me to believe that I was abducted, hauled from one country to the next, and tortured in medieval ways - all orchestrated by the United States government.
"My own despair was greatest when I thought that everyone had abandoned me. I have a duty to make sure that nobody else is forgotten."
Speaking about his period of torture in Morocco, Mr Mohamed said: "I had met with British intelligence in Pakistan. I had been open with them. Yet the very people who I had hoped would come to my rescue, I later realised, had allied themselves with my abusers.
"I am not asking for vengeance, only that the truth should be made known so that nobody in the future should have to endure what I have endured."
Foreign Secretary David Miliband said he was pleased Mr Mohamed had returned to the UK and said it followed "intensive negotiations with the US government".
"In reaching this decision we have paid full consideration to the need to maintain national security and the Government's overriding responsibilities in this regard," he said.
Prime Minister Gordon Brown also stressed that the "security of the country will be protected" but declined to say whether Mr Mohamed would face any restrictions on his liberty.
At a press conference in central London, Kate Allen, director of Amnesty International UK, called for an independent inquiry into Britain's role in secret detention and rendition programmes.
And Clive Stafford Smith, Mr Mohamed's UK lawyer, said he was "absolutely" convinced of the former detainee's innocence.
"If anyone wants to put him on trial, in the immortal words of George Bush, bring them on," he said.
Shadow foreign secretary William Hague told Sky News it was "very important that we get to the root of all this".
"Is he still some kind of security risk, in which case what precautions are going to be taken about it, or is he no risk at all, in which case what has everybody been going on about for the last few years and why has the Government changed their minds?"
Later he also urged the Government to ask for permission to release confidential documents relating to the case.
Mr Hague said: "Given that the Obama administration are reviewing the case of every Guantanamo inmate and have taken a strong stand on torture, and since members of the US Congress are now calling for this information to be released, the Foreign Secretary should ask for the information to be published.
"If they had done this they would not be facing allegations of a cover-up."
He went on: "In order to prevent such a case ever happening again we want to see the current guidance given to officials to prevent torture and cruel, inhuman and degrading treatment when prisoners are not within UK custody or control, but are interviewed by UK officials."
Former Guantanamo detainee Moazzam Begg added that there "has to be" an investigation if the UK wanted to "build bridges" and "to move forward into a better future".
Liberal Democrat foreign affairs spokesman Edward Davey said the Government was now "out of excuses for delaying a full inquiry" and added that "Mohamed's case may just be the tip of the iceberg".
"It is telling that David Miliband is unable to give a straightforward yes or no as to whether British agents and officials have been complicit in torture," he said.
A US Department of Justice spokesman confirmed Mr Mohamed was the first Guantanamo detainee to be transferred under the review of all Guantanamo detainees directed by US President Barack Obama.
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