Two other Sudanese inmates at Guantanamo, Amir Yacoub al-Amir and Walid Ali, were freed along with al-Hajj.
The two said they were blindfolded, handcuffed and chained to their seats during the flight home.
The Reprieve organisation that represents some Guantanamo inmates said Moroccan detainee Said Boujaadia was also released and flown home on the same aircraft as the three Sudanese.
According to a US defence department statement, five detainees were "transferred" to Afghanistan as well. It said that all those detainees, nine in total, had been "determined to be eligible for transfer following a comprehensive series of review proccesses".
Al-Hajj was the only journalist from a major international news organisation held at Guantanamo
and many of his supporters saw his detention as punishment for the network's broadcasts.
Seized in 2001
He was seized by Pakistani intelligence officers while travelling near the Afghan border in December 2001.
Despite holding a legitimate visa to work for Al Jazeera's Arabic channel in Afghanistan, he was handed to the US military in January 2002 and sent to Guantanamo Bay.
Al-Hajj, who is originally from Sudan, was held as an "enemy combatant" without ever facing trial or charges.
Al-Hajj was never prosecuted at Guantanamo so the US did not make public its full allegations against him.
But in a hearing that determined that he was an enemy combatant, US officials alleged that in the 1990s, al-Hajj was an executive assistant at a Qatar-based beverage company that provided support to Muslim fighters in Bosnia and Chechnya.
The US claimed he also travelled to Azerbaijan at least eight times to carry money on behalf of his employer to the al-Haramain Islamic Foundation, a now defunct charity that US authorities say funded armed groups.
The US also clamed he met Mamdouh Mahmud Salim, allegedly a senior lieutenant to Osama bin Laden who was arrested in Germany in 1998 and extradited to the United States.
His lawyers have always denied the allegations.
'Element of racism'
Al-Hajj had been on hunger strike since January 7, 2007.
David Remes, a lawyer for 17 detainees at Guantanamo Bay, told Al Jazeera that the treatment al-Hajj received "was more horrific than most" and that there was "an element of racism" in the way he was treated.
He said he had been in contact with the lawyer representing al-Hajj and it appeared the cameraman had been "psychologically damaged".
"The Europeans would never receive this treatment," Remes said.
About 275 detainees remain at Guantanamo and the lawyer said European detainees had all been returned to their country, leaving nationalities such as Yemenis - who now constitute one third of the inmate population.
Remes said al-Hajj had been released because the Bush administration "wants to flush as many men out of Guantanamo as quickly as possible … as Guantanamo has become such an international badge of shame".
|Amir Yacoub al-Amir and Walid Ali |
were freed along with al-Hajj [EPA]
"Once the Supreme Court said the men could have lawyers the pressure increased [on the US] and condemnation isolated the US administration. Guantanamo was a PR disaster," he said.
"Unfortunately Americans appreciate violations of rights but they have no sympathy for men held at Guantanamo as the [Bush] administration has done such a good job in portraying them as the worst of the worst and as evil doers.
"I've met many prisoners, gotten to appreciate their suffering ... we know them as humans not as worst of worst, we've met their families.
"I've been to Guantanamo and the human dimension of Guantanamo is a story yet to be told," Remes said.
Al Jazeera concerns
Al Jazeera had been campaigning for al-Hajj's release since his capture nearly six and a half years ago.
Wadah Khanfar, the network's director-general who was in Khartoum to welcome al-Hajj, said "we are overwhelmed with joy".
But he criticised the US military for urging al-Hajj to spy on his employers.
"We are concerned about the way the Americans dealt with Sami, and we are concerned about the way they could deal with others as well," he said.
"Sami will continue with Al Jazeera, he will continue as a professional person who has done great jobs during his work with Al Jazeera.
"We congratulate his family and all those who knew Sami and loved Sami and worked for this moment."