Secretary of State Rex Tillerson and AU commission chairman Moussa Faki Mahamat discussed security and counter-terrorism, trade and development, corruption and conflict in an hour-long meeting at the continental body's headquarters in the Ethiopian capital.
But looming over the meeting was Trump's alleged description of African nations as "shithole countries" in January, which forced the president to pen a letter reaffirming his commitment to the continent.
Faki, however, insisted the slur was now in the past.
Tillerson's five-nation Africa tour - to include Djibouti, Kenya, Chad and Nigeria, all key allies in fighting Islamic extremism - has been described by analysts as a "listening tour", with no deals or initiatives due to be announced.
"The purpose of my trip is to listen to what the priorities of the countries here on the continent are and see where there is good alignment," said Tillerson.
Analysts highlight the choice of countries visited by Tillerson as a sign of the United States' focus on security issues on the continent.
Tillerson and Faki discussed continued US support to African counter-terrorism forces in the Sahel and Somalia but no new concrete commitments were given.
"We have not yet won that battle in Somalia and we must stay at it," Tillerson said.
His visit is also a bid to counter the mounting perception that the continent is a low priority for the Trump administration, with US-Africa policy ill-defined and key ambassadorial and State Department posts unfilled.
However he said his visit was "an indication of the importance the continent plays in the future of the US, both in security and from the economic standpoint."
Also looming over the journey is the rise of China as an economic and diplomatic power to rival the West.
Tillerson warned against blind acceptance of booming Chinese investment in Africa.
He said the US was "not in any way attempting to keep Chinese investment dollars out of Africa" but urged governments to "carefully consider the terms of those investments" so they do "not forfeit any elements of your sovereignty".
Tillerson's trip to Ethiopia is scheduled to briefly overlap with a visit by Russian Foreign Minister Sergei Lavrov, who said he had requested a meeting. Washington denied receiving an invitation to talks.
"We sent proposals to the Americans and they said they will think about that but later. As you know, they announced that there will be no meeting and that no discussions (about it) have taken place at all," Lavrov said in Zimbabwe.
Tillerson, in Addis Ababa, called the idea that he had rejected a meeting with Lavrov "silly."
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