"The very country (where) our people were taken as slaves... Has now decided to ban refugees from some of our countries," outgoing AU Commission chair Nkosazana Dlamini-Zuma told some 37 heads of state and leaders from across the continent.
"It is clear that globally we are entering very turbulent times," she added.
Trump's administration has faced outrage and widespread protests over the move to ban citizens from seven countries including Libya, Somalia and Sudan in Africa.
All eyes at the summit are on a bid by Morocco to return to the fold 33 years after it quit in protest against the AU's decision to accept Western Sahara as a member.
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However proceedings began with the swift election of Chadian Foreign Minister Moussa Faki Mahamat, 56, as the new chairperson of the AU Commission, beating four other candidates.
Faki won in a final battle against his Kenyan counterpart Amina Mohamed after seven rounds of voting, the Kenyan government said in a statement, praising a "valiant race" by their candidate.
Faki, a 56-year-old former prime minister, has been at the forefront of the fight against Islamists in Nigeria, Mali and the Sahel and has promised "development and security" will be top of his agenda as chief of the 54-member continental bloc.
He said he dreams of an Africa where the "sound of guns will be drowned out by cultural songs and rumbling factories" and pledged to streamline the bureaucratic AU during his four-year term in office.