"Al-Nusra Front, which has done very well in its jihad) against the tyrant regime of Damascus, should ... remain within the ranks of the Free (Syrian) Army, to maintain unity," the International Union of Muslim Scholars which Qaradawi heads said in a statement.
"This pledge causes internal and external dangers, and its impact on the revolution is dangerous, because it breaks the ranks of the mujahedeen," the Doha-based group said.
Earlier this month, the extremist group pledged allegiance to al-Qaeda leader Ayman al-Zawahiri.
The union urged Al-Nusra Front "to leave the issue of rule and state in Syria until after the liberation, when the people can freely choose an Islamic system or any other system of rule."
It warned that the pledge to Al-Qaeda only "strengthens" the Assad regime.