He and his son Gorka were arrested earlier this month as part of a corruption investigation.
Villar, who denied all the allegations, has been suspended for one year by the Spanish football federation.
"Villar will no longer have any official functions at our organisation," Uefa said on Thursday.
"In view of the ongoing court proceedings in Spain, we have no further comments to make on this matter."
Uefa said its president, Aleksander Ceferin, had accepted Villar's resignation and had thanked him for his years of service to European football.
Villar, a former Athletic Bilbao and Spain midfielder, had headed the Spanish football federation for 29 years. Juan Luis Larrea has been named as interim president.
Suspended Spanish FA boss resigns from Uefa and Fifa
28 July 2017
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Suspended Spanish Football Federation president Angel Maria Villar has resigned from his roles as vice-president of Uefa and Fifa.
