Kenya's government said Mohamed Kuno was behind the attack in April 2015 that killed 148 people.
Regional forces in Somalia said he was one of 16 people killed in an overnight raid on their convoy in Kismayo, a port city in southern Somalia.
Four of those who died were reportedly senior members of the al-Shabab Islamist militant group.
The BBC's Africa security correspondent, Tomi Oladipo, said the news comes as a huge boost for Somalia and its allies in the fight against al-Shabab.
However, at least 10 people were killed on Wednesday by a car bomb outside a hotel in Somalia's capital Mogadishu, that was claimed by al-Shabab.
The news of Kuno's death was confirmed in a press conference held by Abdirashid Janan, the security minister in the Somali region of Jubaland.
After the Garissa attack, Kenya's government put up a $215,000 (£149,000) reward for Kuno's capture.
A Kenyan-Somali, he was a headmaster at a madrassa, or Islamic school, in Garissa until 2007.
But then he crossed the border into Somalia to join the Union of Islamic Courts (UIC), which at one point controlled much of the country.
When the UIC collapsed, he joined the militant group Hizbul Islam, which in 2010 merged with al-Shabab.
He had several aliases but was best known as Mohamed Dulyadin, which means ambidextrous in the Somali language. He was thought to be in mid-30s.
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