The prisoners were the last of the soldiers detained for up to 20 years.
The International Committee of the Red Cross (ICRC) said it had monitored the release in Tindouf, Algeria before being flown to Morocco to be reunited with their families.
It added that the handover followed mediation by the United States.
A government source in Rabat said the prisoners were expected to land in the city of Agadir, about 600km south of the Moroccan capital, soon after 1730 GMT.
Polisario said the release was intended to create an atmosphere helpful to efforts by a newly appointed UN envoy to solve the nearly 30-year-old dispute over the desert territory, mostly held by Morocco but claimed by the Algeria-backed Front.
"This will contribute, we hope, to generating a climate which will favour a dynamic for peace, which we would like to believe will be irreversible," Mohamed Sidati, Polisario's minister delegate for Europe, said in a statement carried by a Norwegian non-governmental organisation that backs the Front.
The release could ease tensions between Morocco and Algeria in a region where the West wants stability because of fears it could be a possible source of Islamic militancy.
Algeria and Morocco have had strained relations since independence from colonial ruler France in 1962 and 1956 respectively.
The Western Sahara dispute has hampered three decades of efforts to normalise ties.
US Senator Richard Lugar, chairman of the Senate Foreign Relations Committee, was to oversee the release on behalf of President George Bush.
It was not immediately clear if he was in Tindouf for the occasion.
Lugar met Algerian President Abdelaziz Bouteflika in Algiers on Thursday, the Algerian news agency APS reported.
He was due in Morocco to meet King Mohammed VI and Prime Minister Driss Jettou, US diplomats and Moroccan officials said.
The senator was also expected to make a statement in Agadir later on Thursday.
Former Moroccan prisoners of war, lobbying for the release of those still held by the Polisario, won support in the US Congress earlier this year.
Spain's withdrawal in 1975 left the Western Sahara divided between Morocco and Mauritania, south of Morocco, and sparked the independence-minded Polisario to rise in an effort to create a Sahrawi Arab Democratic Republic in the former Spanish Sahara.
The Polisario and Mauritania made peace in 1979, and Morocco annexed the desert's southern portion that had been under Mauritanian control.