Mohamed Ibrahim Farah, nicknamed “Gordon”, was killed near Merca, a strategic town captured from the al-Shabab militants in August.
The Somali government army and African Union troops have been battling the al-Qaeda-aligned group for several years.
Al-Shabab has withdrawn from several key towns in recent months, but still controls much of the countryside.
The governor of the Lower Shabelle region in southern Somalia said General Farah was killed along with four other soldiers in an ambush on Sunday.
Al-Shabab still manages to stage attacks in areas it has left, including in the capital, Mogadishu.
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