Araibi, 25, a former Bahraini national youth team player, was granted refugee status in Australia after fleeing charges in the oil-rich kingdom connected to Arab Spring protests.
But he was stopped at Bangkok's main airport at Bahrain's request on November 27 as he arrived in Thailand for his honeymoon.
He was detained in a Bangkok prison pending a court ruling on the extradition request from Bahrain -- a move the footballer had pleaded against saying he fears torture if returned.
Monday brought a stunning about-turn from the Bahraini government, which withdrew the extradition request, said Chatchom Akapin, director-general of the International Affairs Department at the prosecutor's office.
"We have been informed that Bahrain wants to withdraw the (extradition) request... if they don't want him, we have no reason to keep him here," he told AFP.
Just after midnight local time on Tuesday (1700 GMT Monday) the footballer boarded a Thai Airways flight bound for Melbourne.
The Australian government had repeatedly called for Araibi's return and the case had become a cause celebre in the football world, with FIFA also urging the Thai football authorities to intervene.
The international football governing body on Monday thanked Thailand in a statement for "doing the right thing" and said it hoped the athlete "will be able to resume his footballing career soon".
Australian Prime Minister Scott Morrison, who had also repeatedly pushed his Thai counterpart Prayut Chan-O-Cha for Araibi's release, on Monday thanked the Thai government for "listening to the issues" raised by Australia.
"Now the next step is for him to return home. But as it always is in these cases, people aren't home until they're home," Morrison told reporters in a press conference in Canberra.
Former Australian football captain Craig Foster, who has been leading a protest in the sporting community for Araibi's freedom, expressed his "deepest gratitude" for the news.
"My thanks go to the wonderful people of Thailand for your support and to the Thai (government) for upholding international law," Foster posted on Twitter shortly after the news.
Kasit Piromya, a board member of the lobby group ASEAN Parliamentarians for Human Rights, said the footballer's case showed the failings of Thailand's "outdated" laws and policies.
"Hakeem should never have been put through this ordeal in the first place," Piromya said. "Hakeem's case should be a wakeup call to the authorities to change its often cruel and inhumane refugee policies."
Thailand's treatment of refugees has been thrust under international scrutiny in recent weeks.
In January, an 18-year-old Saudi woman who ran away from her family arrived in Bangkok's airport, and armed with a smart-phone and a captive Twitter audience managed to outmanoeuvre Thai authorities and gain refuge in Canada following her pleas for asylum from her "abusive" family.
Bahrain's reversal of Araibi's extradition is surprising.
Only last week the Gulf state issued a statement defending its decision to pursue the footballer after he fled while awaiting trial, and he was convicted in absentia in 2014 for damaging a police station.
But Araibi says the case is bogus and tied to his criticism of Asian Football Confederation (AFC) president Sheikh Salman bin Ebrahim Al Khalifa, a member of Bahrain's ruling family.
A statement from Bahrain's foreign ministry on Monday "takes note of the halt in legal proceedings" though it does not confirm it had withdrawn its extradition request.
"The guilty verdict against Mr. Al Araibi remains in place.... (Bahrain) reaffirms its right to pursue all necessary legal actions against (Araibi)," the statement said.
The reversal came a day after Thailand's foreign minister met with Bahrain's Crown Prince Salman bin Hamad Al Khalifa in Manama to "discuss... areas of interest", according to Bahrain's state-run news agency.