The pair were flown to Bamako using European travel permits or "laissez-passer", not passports or other Malian papers, the government said.
The government said it could not accept people "simply assumed to be Malian".
Recent reports of a deal with the EU to repatriate failed Malian asylum seekers have sparked protests.
In a statement, the Malian government condemned the use of the European "laissez-passez" in cases of expulsion, describing it as "against international conventions".
It also warned airlines not to let people using the document fly to Mali.
The French authorities have not yet commented.
Malians are among the sub-Saharan African nationalities most deported from France: