UEFA also announced Tottenham have been charged over separate crowd disturbances at the Group J game.
A statement from UEFA read: "UEFA has opened disciplinary proceedings against S.S. 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 S.S. 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.