Zahir Belounis, 33, has been repeatedly denied an exit visa until he agrees to drop legal proceedings against his former club, Al-Jaish, over a claim of unpaid wages.
Under the kafala sponsorship system used by many Qatari employees, a player who is employed by a club must obtain an exit permit from his employer in order to be able to leave Qatar.
FIFPro is to provide Belounis with money from its hardship fund and the union's secretary general, Theo van Seggelen, has written to Blatter asking "FIFA's urgent intervention".
A statement said: "FIFPro insists that Belounis be allowed to leave Qatar and receive his wages immediately. At the very least he should be freed, able to play for a new club and be guaranteed that he can claim his unpaid salary in a case before FIFA's dispute resolution chamber (DRC).
"Without income for a prolonged period and forced to sell off most of his personal possessions, Belounis and his family are said to be living in an apartment with no furniture which they must vacate in a matter of days.
"As a result, FIFPro will offer financial assistance from its hardship fund to help the Belounis family find accommodation. These funds will be made available immediately."
FIFPro is also sending board member Mads Oland, plus representatives from the International Trade Union Confederation (ITUC), to travel to Qatar to meet with the Belounis family and pressure the Qatari government to allow them to leave.