European football's governing body confirmed on Tuesday they have charged the Rome club for the 'racist behaviour' of their fans during last Thursday's 2-0 win over Borussia Monchengladbach as well as the 'throwing of missiles and or fireworks' and 'insufficient organisation'.
Lazio fans were found guilty of similar racist offences in the home and away ties against Tottenham and the game with Maribor.
Following the game in Slovenia, UEFA suspended a sanction of playing a Europa League tie behind closed doors for a probationary period of two years.
That could now be imposed when UEFA's Control and Disciplinary Body meet on Wednesday and could mean the Stadio Olimpico is empty when Lazio host Stuttgart on March 14 in the second leg of their last-16 tie.
Monchengladbach also face a charge after their fans lit fireworks in the stadium as Lazio advanced 5-3 on aggregate following a 3-3 draw in the first leg.
The build-up to the match was overshadowed by trouble with 8,000 German fans having descended on Rome.
Three Monchengladbach fans were stabbed in confrontations although none of the injuries were serious.
Lazio president Claudio Lotito was dismayed by the latest outbreak of violence although he felt it was unfair to blame the club.
He told Sky Sport Italia: "I would urge the media not to label the protagonists of all these incidents as 'Lazio fans'. Rome is a metropolis and as such is inhabited also by bad people.
"For example, there is no suggestion so far that those behind these incidents were part of Lazio's organised fan groups.
"Nobody is trying to justify this behaviour, but I say this because I am in constant contact with the police and want to understand if these people really are linked with Lazio.
"In my view they should do a quick trial and send them to prison for some time, so they don't have the chance to do it again."