Mr al-Araibi boarded a Thai Airways flight just after midnight local time and is expected to arrive in Melbourne this afternoon.
The player's Australia lawyer Latifa Al-Haouli of Sabelberg Morcos Lawyers, told SBS News on Monday legal staff were working with Thailand's department of corrections to secure Mr Al-Araibi's return to Australia.
The Pascoe Vale FC footballer has been given political asylum in Australia as a refugee since fleeing Bahrain five years ago after he was jailed and tortured for protesting against the Bahrain government.
He also believes he was targeted for arrest because of his Shiite faith and because his brother was politically active in Bahrain.
Alqunun fled her family to Bangkok while on holiday in Kuwait but was detained by authorities shortly after arrival.
Thailand's Ministry of Foreign Affairs said it had no comment on the case.
A similar campaign was launched on behalf of Araibi by human rights groups, fellow soccer players and other activists - including the heroes who helped save a Thai soccer team trapped in a cave past year - with the hashtag #SaveHakeem.
The state-run Bahrain News Agency (BNA) reported on Sunday that Prime Minister Khalifa bin Salman Al Khalifa had a phone call with Thai Prime Minister Prayuth Chan-ocha, but offered no details of their discussions.
Bahrain has a Shia majority but is ruled by a Sunni monarchy.
The Bahraini government had insisted that he should be treated as a simple fugitive and will have an opportunity to appeal his conviction in the country's courts.
The move comes just days after the two Australians who helped mount the Thai cave rescue, Australians of the Year Craig Challen and Richard Harris, sent a letter to the Thai government, pleading for mercy for Hakeem.
He had faced at least another two months in jail after a court in Bangkok last week set down his pre-trial extradition hearing for April 22.
But tonight Thai authorities finally relented after Bahrain apparently dropped their extradition demands and allowed Hakeem to be released.
"This is a win for humanity, for the power of citizens of the world demanding that human rights be protected", Foster said in a statement.
He said Federation Internationale de Football Association has not discussed imposing sanctions on either Bahrain or Thailand over the case.
Chatchom added that the process to release Araibi is underway.
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