Tottenham have also been charged over separate crowd disturbances following the match on November 22.
Lazio supporters mocked Spurs' links with the Jewish community by chanting "Juden Tottenham" at the away fans during the 0-0 draw at the Stadio Olimpico on November 22.
A UEFA statement said: "UEFA has opened disciplinary proceedings against SS Lazio.
"Charges relate to the alleged racist behaviour of Lazio supporters during the Italian club's 0-0 UEFA Europa League Group J draw against Tottenham Hotspur FC in Rome on 22 November 2012.
"Proceedings will also be instigated against SS Lazio for throwing of missiles and/or fireworks by their supporters, incidents of a non-sporting nature, late team arrival at the stadium, and late handling of the team sheet."
UEFA will hear both cases at a disciplinary meeting on January 24.
This is not the first time the Italian club have been accused of racism this season.
In the reverse fixture at White Hart Lane back in October Lazio's fans were found guilty of monkey chanting towards three Tottenham players.