The away fans stormed the pitch, clashing with riot police in Vilnius after watching their team concede two first half goals to the Lithuanian minnows through Brazilian Lima Severino and midfielder Dejan Milosevski.
UEFA's disciplinary board will discuss the match and the punishments set to be dished out to the Polish outfit. The results of which will certainly hand a first leg victory to FC Vetra and could see Legia Warsaw disqualified from the competition.
Legia have until Tuesday to submit a statement.
Blackburn Rovers will be eagerly awaiting the outcome of the meeting as they will face either FC Vetra or Legia in the third-round.