Muktar Robow was the subject of a $5 million bounty from the United States for his role with the Al-Qaeda linked Islamist militants.
But his split with former Shabaab leader Ahmed Abdi Godane four years ago led him to seek safety in his hometown in Somalia's southwest Bakool region, though he never formally renounced the insurgency.
"Muktar Robow defected from Shabaab and he is now in Hudur meeting with government officials," district commissioner Mohamed Moalim told reporters, referring to the Bakool district capital.
Godane was killed by a US air strike in 2014, but the bad blood between the militants and Robow appeared to have continued.
A security source told AFP Robow's surrender came after Islamist militants attacked him last week.
His name also no longer appears on the US's Rewards for Justice wanted list.
The defection is a blow to Shabaab, which remains deadly in Somalia despite the presence of a 22,000-strong African Union force dedicated to fighting it and supporting the internationally backed government based in Mogadishu.
Uganda's military last month said 12 of its soldiers had been killed in Somalia in an ambush claimed by the group.
Shabaab has also carried out attacks in Kenya and Uganda, both contributors to the AU force.