Ahmed Diriye, who took over as the militant group's leader in September 2014, and intelligence chief Mahad Karate, were both designated as terrorists by the State Department.
US officials said the group was behind several atrocities, including the 2013 Westgate Mall attack in Nairobi and the April 2 massacre at Garissa University in Kenya in which 148 people were killed.
Yesterday's attack on a UN staff bus in the northeastern Somali town of Garowe killed seven people including four staff working for the children's agency UNICEF. Four other UNICEF workers were in a serious condition.
The Shebab, meaning "youth", emerged out of a bitter insurgency against Ethiopia, whose troops entered Somalia in a 2006 US-backed invasion to topple the Islamic Courts Union that was then controlling the capital Mogadishu.
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Shebab rebels have staged frequent attacks in their fight to overthrow Somalia's internationally-backed government, as well as to counter claims that they are close to defeat due to the loss of territory, regular US drone strikes against their leaders and defections.
They have also carried out revenge attacks across the wider region against countries which contribute troops to the 22,000-strong African Union force in Somalia, AMISOM.
"He shares Godane's vision for Shebab's terrorist attacks in Somalia as an element of Al-Qaeda's greater global aspirations," the State Department said in a statement.
Karate, also known as Abdirahim Mohamed Warsame, "played a key role in the Amniyat, the wing of Shebab responsible for the recent attack on Garissa University College in Kenya," it added.
The Shebab was designated a foreign terrorist organization by the United States in 2008.