The heavily armed reinforcements arrived in pickup trucks mounted with heavy machine guns.
Fighters from both sides closed in on each other following a night of artillery exchanges that sent thousands of civilians fleeing the Sii-Sii neighbourhood of northern Mogadishu.
Residents in the Somalia capital described it as the worst fighting in more than a decade of lawlessness. Thousands of families were fleeing the capital.
While tending to his wife in the hospital, Mohamud Jama said his three children were killed when three mortar rounds struck his house.
"This is the first time we have witnessed people fighting in Somalia and targeting civilians in such a savage way," Mr Jama said.
Machine gun, rocket and mortar fire rained down on bullet-scarred neighbourhoods in northern and central Somalia, indiscriminately killing and wounding civilians while residents fled their homes in terror, witnesses said.
Overnight violence claimed at least 17 lives as shelling of urban residential areas intensified and eight people died later as the two factions showed no sign of heeding widespread appeals for a truce, they said.
"Seventeen people were killed overnight, mostly by heavy mortar shells," Ahmed Idriss, a Somali peace activist, said, adding that another 36 had been wounded and taken to hospitals.
Four civilians and four gunmen - three alliance fighters and one Islamist - were later confirmed killed by sources on both sides.
Meanwhile, thousands of civilians fled the most-affected Huriwa, Yaqshid, Waharaade and Sisi neighborhoods, leaving up to 70 percent of homes empty amid the continuing chaos, residents said.
"There is very heavy fighting here with huge shelling," said Huriwa resident Abdinasir Mohamed. "We haven't seen many fighters today but the shelling has been going on since last night. We don't know what to do."
Nowhere safe
"We don't know where to go, where is safe," said shop owner Maryan Ibrahim.
"There is violence in many parts of the city and we are anticipating more. Huriwa is bad, Sisi is the worst and Karan is also bad."
The International Committee of the Red Cross (ICRC) estimated 80 people had been killed, citing a survey of the city's hospitals, two of which reported treating at least 184 wounded people, including 20 women and 22 children.
In a statement, the ICRC and Somali Red Crescent said they were increasingly concerned about the humanitarian consequences "of the intense armed clashes" in Mogadishu.
Similar expressions have already come from the United Nations and Somalia's largely powerless transitional government that is currently based in the town of Baidoa, west of the capital Mogadishu, both of which urged calm.
The appeals and an offer of a truce from the Islamic clerics who control the militia were dismissed by the warlord-led Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT), which blamed the Islamists for the violence.
"Most of the indiscriminate shelling is coming from the so-called Islamic courts who have no regard for humanity," alliance spokesman Hussein Gutale Raghe said, adding that his group would fight until the Islamists were defeated.
But an official of Mogadishu's increasingly influential courts, which UN experts believe now control of about 80 percent of the capital, placed the blame squarely on the alliance, which was formed in February with US support.
"You know who is paid to kill Somalis by outsiders," the said.
"The courts are out to save the Islamic people of Somalia, and our ceasefire offer was rejected by the so-called alliance."
The violence has now eclipsed that recorded over three days in February and four days in March when at least 85 people were killed as the two factions fought each other.
Those incidents had been the bloodiest clashes in the capital since Somalia collapsed into anarchy 15 years ago and sent tensions skyrocketing with the Islamic courts declaring a "holy war" against the ARPCT.
The alliance has vowed to curb the power of the courts that have gained popular backing by restoring some stability to areas in Mogadishu they control by imposing Sharia law.
It also accuses the courts of harbouring terrorists and training foreign fighters on Somali soil, charges that Islamic leaders deny but are also levelled by the United States and other Western nations.
Although Washington has not explicitly confirmed its support for the
alliance, US officials have said the group has received US money and is one of several it is working with to contain the threat of radical Islam.
Last week, the State Department acknowledged that the United States was working with "responsible individuals" in Somalia to prevent "terror taking root in the Horn of Africa."