The punishments, like others carried out by the Islamists in their sharia courts in the capital Mogadishu and elsewhere, follow the naming of Sheikh Hassan Dahir Aweys - on a UN list of al Qaeda associates - to a top post over the weekend.
Aweys, a former army colonel who in the 1990s led militant Islamists in failed campaigns in Somalia but has denied any al Qaeda links, was named head of the Council of Islamic Courts.
The council is a parliament for the Islamists, whose well-trained militias seized Mogadishu from US-backed warlords on June 5 after months of fighting that killed at least 350.
The rapists were to be stoned to death in Jowhar, which the Islamists took in the last phase of a campaign that saw them seize a strategic swathe of Somalia from the coastal capital northwest nearly to the Ethiopian border.
''Five men who raped four women on June 22 will be stoned to death today in accordance with the Islamic sharia. They have pleaded guilty to the crime and also have been identified by the victims,'' Siyad Mohamed, a militia leader linked to Islamic courts, told Reuters by phone from Jowhar.
The Islamist victory dealt an embarrassing public setback to Washington's counter-terrorism campaign, as its support for the much-despised warlords gave the Islamists popular backing that propelled their ascendancy.
'THE UPPER HAND' The Islamists at first tried to present a moderate face to the world, saying they only wanted to end anarchy and restore peace lost since dictator Mohamed Siad Barre's ouster in 1991.
One Western diplomat who follows Somalia said Aweys' rise would likely close channels for dialogue with the West.
''I think it demonstrates how secure they feel in their own right. They don't need international recognition, and they can do this because they have the upper hand,'' the diplomat said.
The shooting of a Swedish journalist in Mogadishu on Friday also hurt the Islamists' claim to be pacifying the city.
Asked about the appointment of Aweys, Somalia's interim government was circumspect: ''It is the internal business of the courts,'' government spokesman Abdirahman Dinari said.
Somalia's weak interim government and the Islamists, in talks mediated by Sudan in Khartoum, last week agreed to recognise each other and meet again on July 15. Both sides are deeply suspicious of the other's intentions.
Court sources have said there is a split in the Islamist ranks between moderates and hardliners like Aweys, who want an Islamic state.
Aweys is a former leader of al-Ittihad al-Islami, which fought for that cause in the 1990s but was defeated by Ethiopia and also warlords Addis Ababa had backed - including Somalia's current interim president, Abdullahi Yusuf.
An Aweys protege, Aden Hashi Ayro, is an Afghanistan-trained militia commander linked to the killings of aid workers and at least one journalist there in recent years, and the desecration of an Italian cemetery in Mogadishu last year.
Western diplomats and security experts say he has al Qaeda connections and that there are training camps and a handful of the group's operatives in Somalia, but the Islamists deny it.
Reuters SHR BD1847