Sharif Hassan Shaikh Aden was elected speaker on Wednesday with 161 votes, beating 10 other contestants from five clans in Somalia.
In all, 267 of the 275-member assembly voted when lawmakers met on the southern outskirts of the Kenyan capital of Nairobi.
The parliament, sitting in Nairobi instead of the Somali capital Mogadishu due to security concerns, was being presided over by Hirsi Bulhan Farah, who was elected early this month on a temporary basis.
"What is of paramount importance is that Somalia gets a government to stand on its feet again," Aden, who is a businessman based in Dubai, said.
"The exercise was very democratic ... I promise to work with all those who voted for and against me," he said.
Aden will act as the head of state until the lawmakers vote in a president on 22 September.
But Aden's victory was tainted by allegations of fraud by a losing candidate.
"There was absolute corruption here," Muhammad Nur said. "I will not accept losing this election."
Somalia is the only country in the world without a government for the last 13 years.
Lawless Somalia is regarded as a
classic example of 'failed state'
The transitional parliament was inaugurated on 22 August and is due to last for an initial period of five years before elections are to take place.
No functional parliament or government to speak of has existed in Somalia since 1991, the year controversial president Muhammad Siad Barre fled the country amid clan warfare.
There followed 13 years of factional bloodletting that turned Somalia into the archetypal "failed state".
Aden's election coincided with heavy fighting that erupted in Somalia's Lower Juba region between supporters of two warlords, leaving behind an unknown trail of casualties.