The battle, which erupted on Wednesday and has killed at least 70 people so far, had eased overnight.
But fighting broke out in the Daynile and Keysaney districts on Saturday, sending terrified residents fleeing, witnesses said.
On the other side of the shattered city in Galgalato, fighters for warlords, who have dubbed themselves a counter-terrorism alliance, repelled attacks from Islamist militias who have increasingly gained control of Mogadishu.
"We are hiding for our lives," said Abdirahman Hussein, a resident who said he and others in the area spent a sleepless night as mortars and artillery shells pounded their neighbourhood.
Retaking lost territory
The warlords - among them four ministers in Somalia's weak transitional government - said they were trying to retake areas seized from them on Friday.
"It is another fight we must have, to get back our territory at Kilometre 4," Abdullahi Atosh, the warlord militia leader, said as he re-organised his force in the Bulo Hubey area of Mogadishu, where his forces retreated on Friday.
Kilometre 4 is a critical junction and had been a warlord stronghold until the Islamist militias routed them and seized the Sahafi hotel owned by a warlord.
The Islamists, backed by influential sharia courts, have taken greater control of the city every time they have clashed with the warlord coalition since its formation in February.
This is the fourth round of fighting between the two sides since February, in what residents say is the worst combat in the city in a decade.
At least 320 people, mostly civilians, have been killed and hundreds wounded.