The removal of the five civilians from the Sovereign Council came after General al-Burhan said on Monday the army would not participate in internationally led dialogue efforts to break its stalemate with the civilian opposition.
The junta boss urged political and revolutionary groups to start talks to form a transitional government.
The general said the Sovereign Council would be disbanded, replaced by a "Supreme Council of Armed Forces" controlling both security and defense.
The new body would include both the regular military and its Rapid Support Forces, a paramilitary unit commanded by a Burhan deputy, Hamdan Daglo.