Jawari's previous term as speaker was characterised by political wrangling and grindingly slow legislative progress
The re-election of former speaker Mohamed Osman Jawari took place at a heavily-guarded police academy in the capital Mogadishu where he won 141 votes from 259 MPs, enough for a first-round victory, according to Osman Elmi Boqore who chaired the session.
Fears that Somalia's Shabaab insurgents might target the election meant the area close to the voting was on lock-down with many other roads around the city also closed to civilian vehicles.
Clan is the organising principle of Somalia's politics with influential roles such as speaker, prime minister and president divided among the main clans.
The election of 71-year-old Jawari, a member of the Digil and Mirifle clan, means that his fellow clansman, the president of Somalia's federal South West state, Sharif Hassan Sheikh Adan, will be forced to withdraw from the presidential race.
The remaining frontrunners are from two of the major clans, the Hawiye and Darod.
Current President Hassan Sheikh Mohamud, a 61-year-old former academic and civil society activist from the Hawiye clan is seeking re-election.
Also in the running is ex-president Sharif Sheikh Ahmed, a fellow Hawiye and 52-year-old former leader of the Islamic Courts Union which pacified Somalia before being driven out by US-backed Ethiopian troops.
The leading Darod candidates are the current Prime Minister Omar Abdirashid Ali Shamarke, 56, and a former prime minister Mohamed Abdullahi Mohamed 'Farmajo', 55. Both hold dual nationalities having lived for years in Canada and the US respectively.
Jawari's previous term as speaker was characterised by political wrangling and grindingly slow legislative progress, but he cemented his reputation as an outspoken politician who took a tough stance on disputes in parliament.
"I promise to lead the house of the people with integrity," Jawari said after his election.
The election of the parliamentary speaker marks the beginning of the end of Somalia's drawn-out electoral process that saw 14,025 delegates voting for 275 parliamentary seats distributed according to clan with the 72 seats in a new upper house shared out according to region.
Some seats remain unfilled, but sufficient lawmakers were sworn in late last month to move forward with votes for speakers of both houses and the presidency, expected later this month.
Somalia has not had an effective central government since the 1991 overthrow of president Siad Barre's military regime which ushered in decades of anarchy and conflict in a country deeply divided along clan lines.
The clan rivalries and lawlessness provided fertile ground for the Al-Qaeda linked Shabaab to take hold and seize territory, frustrating efforts to set up a central administration.
After a series of transitional governments were formed abroad, a previous parliament was chosen by 135 clan elders and set up in Mogadishu in 2012.
The 2016 process is seen as taking the country a step closer to a universal suffrage election now planned for 2020.