More than 1600 of them were sent back to Mali and Senegal from Oujda, a communications hub near the frontier with Algeria in northern Morocco before operations were switched over the weekend to a military base outside this town in the far south of Morocco.
The airlifts are part of the north African kingdom's response to a surge of illegal immigration, which has led to violence around the Spanish enclaves of Ceuta and Melilla, where at least 14 people have been killed in attempts to storm the frontiers.
Hundreds of destitute west Africans were brought to Guelmim aboard convoys of buses after being rounded up in the north.
According to Sunday's official figures, 1117 Senegalese and 1031 Malians have so far been sent home aboard 15 flights.
The governor of Guelmim said operations were to continue for two or three more days following three flights Saturday and a further flight during the night of Saturday-Sunday.
The expulsions have been taking place in the presence of diplomats from the countries of destination.
A Moroccan government source said Foreign Minister Foutouma Sidibe of Guinea was scheduled to arrive to supervise the departure of 93 of her compatriots.
A security source said the expulsion of hundreds of Africans from other countries in the sub-continent was scheduled to get under way later this week.
Moroccan Interior Minister Moustapha Sahel has estimated that about 15,000 migrants are still illegally in Morocco, in addition to 25,000 sub-Saharan Africans who live in the country illegally.