It will be Emery's second spell in the Premier League, having coached Arsenal in 2018-19.
Emery replaced Steven Gerrard, who was fired last week after a year in charge.
Villa said Emery will start as manager on Nov. 1 after his work permit formalities are completed.
Emery had been with Villarreal since July 2020. He was previously coach of Paris Saint-Germain and Sevilla.