Sheikh Hassan, a local elder loyal to the Islamic courts group, said on Wednesday: "At last we are in the town".
The Islamists' capture of Jowhar gives them control of most of southern Somalia and raises the question of whether they will help the interim government or impose Islamic rule.
Islamist militia sources in Nairobi said four people were killed and 10 to 18 were wounded.
Wednesday's assault appeared to be an attempt to deliver a final blow to the weakened regional commanders, whose control of patches of Somalia including Mogadishu for the past 15 years has taken a turn for the worse.
Residents said militia fighters linked to sharia courts had seized Jowhar airport to the west of the town, about 90km from Mogadishu.
They also entered from the south, sending residents fleeing as they attacked the town with heavy artillery and machine guns.
The regional commanders' fighters - in this case hired guns linked to the local administration and remaining commanders including Mohamed Dheere - dropped their weapons and fled.
Somali militiamen belonging to
the Islamic fighters' faction (file)
Hours before fighting began in Jowhar, four comanders who had gone there from Mogadishu fled from the town, and a main ally said he was abandoning their cause.
However, a leader of the militia fighters dislodged from Baidoa, where Somalia's interim government had set up its base, said they were regrouping to attack the town, which is 240km (150 miles) northwest of the capital, Mogadishu.
The government of the president, Abdullahi Yusuf, had set up its own militia in Baidoa to provide security.