Mr Hersi, a leading figure in the militant group's intelligence wing, surrendered to police in the Gedo region, local media report.
In June 2012, the US state department offered $3m (£1.9m, 2.5m euros) for information leading to his capture.
It comes three months after al-Shabab leader Ahmed Abdi Godane was killed in a US air strike.
A Somali intelligence officer, quoted by the Associated Press news agency, suggested Mr Hersi may have surrendered because of a dispute with al-Shabab members loyal to the former leader.
BBC Africa editor Mary Harper says Somali intelligence had received a tip off that he was hiding in a town close to the border with Kenya.
He fell out with Godane last year and has been on the run ever since but he is still a powerful figure, she adds.
Ahmad Umar was named the new leader of al-Shabab, days after Godane's killing last September.
The US has supported the African Union (AU) force that has driven al-Shabab out of the capital Mogadishu and other towns since 2011.
The al-Qaeda-linked fighters want to overthrow the UN-backed Somali government and frequently attack government targets as well as neighbouring countries that provide troops to the AU force.
Three members of the AU force and a civilian contractor were killed in an al-Shabab attack on its headquarters in the capital Mogadishu on Thursday.