Egypt's major archaeological sites were targeted for looting after the 2011 uprising that toppled former president Hosni Mubarak.
Thousands of artefacts, most obtained from illicit digs, later surfaced on the international market, at auction and on websites.
The 123 artefacts to be returned were "illegally taken outside Egypt, and have been confiscated by the US customs authority in New York," Antiquities Minister Mamdouh al-Damati said in a statement.
"Egypt proved its ownership of the artefacts and the United States has decided to return them."
Officials say the artefacts will be repatriated in the next few days.
Egypt has signed several agreements that enable it to reclaim such ancient pieces after proving their ownership and that they had been smuggled abroad.