The unrest occurred ahead of kickoff at Villa Park, and the police denied entry to travelling fans, leaving the away stand empty. Villa won the match 2-1.
"Aston Villa can confirm it has lodged an official complaint with UEFA over the conduct of Legia Warsaw Football Club and the behaviour of their supporters prior to last night’s UEFA Europa Conference League match at Villa Park," Villa said in a statement.
Legia Warsaw said Aston Villa had given the Polish club a lower allocation of tickets than they were entitled to under UEFA regulations.
In Friday's statement, Villa said Legia Warsaw had been informed of the ticket allocation details four weeks before the match, adding that the Polish team's officials had refused to confirm if they would accept their allocation until 4pm on Thursday.
"The lack of cooperation and prevarication from Legia Warsaw officials prior to the match was entirely unacceptable and deeply disappointing," said Chris Heck, President of Business Operations at Aston Villa.
"This behaviour increased the danger that West Midlands Police officers and our own fans were subjected to before the game and the scenes of disorder from the Legia fans have no place in modern football or civilised society."
Reuters has contacted Legia Warsaw for comment.
Earlier on Friday, police said they had arrested 46 people following the clashes.
"We've now got 46 people in custody following last night's violence involving away fans outside Villa Park," West Midlands Police said in a statement.
"Officers faced 90 minutes of sustained violence, and four were injured.
"We're proud of our officers, and thank Aston Villa fans for their support."
