"Both were arrested due to their possible ties with different suspects in this case," a statement from the prosecutor said.
The suspects were identified as Belgian national Zakaria J., who was born in 1986, and Moroccan national Mustafa E., who was born in 1981.
Neither weapons nor explosives were found in the raids
French President Francois Hollande has said that the Paris attacks were planned in Syria but prepared and organised in Belgium.
The Islamic State group has claimed responsibility for the attacks.
Last week the authorities announced that Belgian police have identified three safe houses used by key suspects including presumed ringleader Abdelhamid Abaaoud, who was also a Molenbeek resident
He was killed in the French police raid days after the Paris attacks.
The Belgian authorities have formally charged 10 people in the case, including a number from Molenbeek.
Four suspects remain at large, including Salah Abdeslam who allegedly drove suicide bombers to the French national stadium outside Paris, as well as Mohamed Abrini, suspected of having helped scout out the attack sites.
Both are from Molenbeek.