Belounis will land in Paris on Thursday evening, his brother said.
FIFPro and others lobbied for Belounis to be allowed to leave.
"As the worldwide representative for professional footballers, FIFPro will be able to welcome back a long-lost family member," the union said in a statement.
Still, FIFPro is going ahead with its four-day visit from Thursday to the Gulf state "in a bid to help prevent future misery for those who find themselves powerless under the working conditions of Qatar's kafala sponsorship system."
Mahdi Belounis said the pressure was vital in convincing Qatari officials to let his brother leave.
"They realized they were destroying their image," Mahdi Belounis said. "The pressure from FIFPro was the straw that broke the camel's back. They said to themselves, 'We've got to put a stop to this and give him an exit visa.'"
Zahir Belounis claimed Qatari officials withheld the visa to punish him for trying to recover wages he said he was owed.
His case highlighted the "kafala" employment system in Qatar, which stops workers from leaving without written permission from employers. It also handed ammunition to critics who accuse Qatar of not respecting the rights of migrant workers.
"This system is slowly killing me and many other people risk suffering in the same way," Belounis wrote in an open letter, published in The Guardian newspaper this month and addressed to France great Zinedine Zidane and Bayern Munich coach Pep Guardiola in a plea to intervene on his behalf.
"I haven't seen my family in France since June 2012 because my employer refuses to give me the exit visa," he wrote. "I am not alone in this predicament. Many workers who are to build the stadiums for the 2022 World Cup risk finding themselves in the same situation as me."
"If Qatar does not scrap its 'exit visa' system, then there will be hundreds, maybe thousands, of people trapped here," Belounis argued.
