Godane, for whom the US have offered $7 million, earlier this month ordered the arrest of Afghani and at least a dozen other leaders, according to security sources.
Shabaab gunmen also killed Abdi Hamid Hashi Olhayi, named as another senior commander and co-founder of the group.
Long active mainly in southern and central Somalia, the Shabaab have had a string of key towns wrested from their control by a 17,700-strong African Union force, fighting alongside government troops.
The Shabaab is fractured into multiple rival factions, some based along clan lines and others ideological.
Some are more attracted by a nationalist agenda to oust foreign forces from Somalia, while others – including Godane – have more international jihadist ambitions.
The deaths show the splits in the long-running insurgency whose aim is to topple the internationally-backed government, but also signal Godane’s efforts to sweep away opposition to his command and cement his more radical leadership.
But analysts warn that the divisions among the Shabaab do not necessarily dent its strength.
Earlier this month the Shabaab showed their strength with a brazen daylight attack on a fortified United Nations compound in Mogadishu, with a seven-man suicide commando blasting into the base and starting a gun battle.
The complex attack on the UN killed 11 and used tactics already tried in April when the Shabaab attacked a Mogadishu court house.
“The evolution of the Islamist group appears to be aiming at a future objective where it might not be in charge of the country, but where it could make the country ungovernable,” South Africa’s Institute for Security Studies (ISS) warned earlier this month.
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