Al Jazeera identified the Aweys-led wing as the Somali Islamic Front and quoted a leader of the group, Abdullah Ahmed Omar, as pledging to intensify "jihad until the liberation of Somalia from the enemy".
But Sheikh Sharif Sheikh Ahmed, the ARS leader, who was chairing a meeting of the group in Djibouti, dismissed the move.
"What they have said is null and void," Suleiman Olad Roble, a spokesman for Ahmed, told the AFP news agency.
Ahmed and Aweys fell out after Sharif decided to participate in recent UN-sponsored peace talks in Djibouti, to seek an end to the fighting in Somalia.
The ARS was formed in September 2007 in Asmara and delegates chose Ahmed as its new leader.
The ARS central committee, under Ahmed's leadership, has endorsed a June 9 ceasefire agreement reached with the transitional government at the Djibouti talks.
However, Aweys has rejected the truce, insisting that the ARS is committed to driving out Ethiopian forces who entered Somalia in late 2006 and ousted the Islamic Courts' Union from the country's south and central regions.
Numerous internationally-backed peace-making initiatives have failed since the country plunged into lawlessness 17 years ago.
Testifying to Somalia's continued instability, residents of ts capital Mogadishu said on Tuesday that clashes in and around the city left three soldiers and two fighters dead.
Two more soldiers were killed when fighters attacked them in northern Mogadishu's Yakshid district, witnesses said.
"The two soldiers were killed by three men armed with pistols as they were walking to their station," Mohamed Ayanle, resident, said.
A Somali military commander said that government forces had killed 12 fighters, including two foreigners.
But the Harakat Shabab Al Mujahid (Jihadist Youth Movement) denied the commander’s statement.