Residents reported several loud explosions near the al-Yarmouk barracks in the Salaheddin district. Gunfire and explosions later appeared to die down.
Heavy fighting involving anti-aircraft batteries also broke out near an army camp in Tajoura, an eastern suburb.
It was unclear who was involved in the latest violence, which killed at least two people from Mali, a health ministry source said.
Haftar and other militias have demanded that parliament step down. But Islamist-leaning brigades and the Muslim Brotherhood have called for militias to protect government institutions.
On Sunday the national election commission proposed holding parliamentary elections on June 25, an attempt to ease tensions.