A Defence Ministry official in Kabul said governor Ismail Khan's forces were now in the control of Zahir Nayebzada's troops. "The fighting has ended, the division has been overrun," he said.
Tank and gun battles erupted on Sunday in the western city of Herat between troops loyal to Nayebzada, a commander recently appointed by President Hamid Karzai, and those of governor Khan.
Khan's son, Civil Aviation Minister Mirwais Sadiq, died after a rocket-propelled grenade hit his car in Herat on Sunday. Khan's forces blamed Nayebzada.
"Nayebzada and his supporters have fled, we don't know where; some of his men surrendered to us," said Khan's spokesmen Ghulam Muhammad Masoan. He said 10 of Khan's men had been killed.
Nayebzada told Reuters on Sunday more than 100 people on both sides had died. He could not be reached on Monday.
The Pakistan-based Afghan Islamic Press quoted sources in Herat as saying more than 100 had died and many more wounded. It said bodies were strewn around the base of Nayebzada's division and many dead and wounded had been brought to hospital.
"Nayebzada and his supporters have fled, we don't know where; some of his men surrendered to us"
Ghulam Muhammad Masoan,
spokesman for Ismail Khan
Khan has been at odds with Karzai's US-backed government in the past for failing to hand over tens of millions of dollars of customs revenues from Herat, which controls the bulk of Afghanistan's trade.
A veteran of the struggle against Soviet rule in the 1980s, Khan professes loyalty to Karzai, but has often been accused of running a personal fiefdom in the west.
The fighting was among the worst between pro-government factions since Karzai was installed to power after US-led forces ousted the Taliban in 2001, and underscored his difficulties bringing stability to the war-ravaged country.
An Afghan aid worker said the battles that had raged in several areas of the city had died down after midnight, but many residents were staying at home. He said the fighting had involved tanks, mortars and artillery.
The halt to the fighting came shortly after the US embassy issued a statement urging all involved to remain calm.
Karzai chaired an emergency National Security Council meeting on Sunday and a presidential spokesman said government troops would be sent to restore order. He warned of "severe" action unless the fighting stopped.
Nayebzada said on Sunday he had acted in self-defence after Khan's forces tried to take control of his division and Sadiq attacked his house. "I did not kill Sadiq in an ambush; he was killed in a clash afterwards," he said.
Ismail Khan is the governor of
the western Herat province
A Khan loyalist said Sadiq was killed while investigating an incorrect rumour that his father had been ambushed.
The US embassy expressed concern about the violence, which it said appeared to have begun as a "traffic incident".
"Afghans must not let the success of the last two years be put in jeopardy by this incident," it said, underscoring the risks to US efforts to stabilise the country.
About 100 US soldiers and State Department personnel are in Herat as one of the US military's provincial reconstruction teams, and tasked with bolstering security.
The US heads a 13,500-strong foreign force hunting Taliban and al-Qaida fighters which has also been taking a wider security role ahead of elections, supposed to be held in June.
Sadiq was the third member of the cabinet and the second civil aviation minister to be killed since Karzai's government came to power in place of the Taliban in late 2001.