The Rome club was also fined by the Italian league on Monday for a separate incident involving racist abuse.
In addition to the alleged chants, Lazio fans displayed a "Free Palestine" banner at the Olympic Stadium on Nov. 22, apparently taunting Tottenham, which draws fans from London's Jewish community.
UEFA said its disciplinary panel will judge the case on Jan. 24.
Lazio could be ordered to play its next Europa League home match in an empty stadium. It faces Borussia Moenchengladbach in the last 32, with the second leg in Rome on Feb. 21.
Lazio was meanwhile fined €15,000 ($20,000) by the Italian league for racist chants by its fans directed at Cagliari's Colombia forward Victor Ibarbo in Saturday's match, which Lazio won 2-1.
UEFA has already fined the Italian club €40,000 ($52,300) for its fans' racist behaviour when it played Tottenham in London in September.
UEFA acted on the second incident after receiving reports from the English Football Association and the European fans' network FARE, which sends monitors to high-risk games.
The return leg, which ended 0-0, was played amid tension after attacks on Tottenham fans in a bar in central Rome.
UEFA said that Lazio faces a range of charges, including fans throwing missiles and fireworks. The team also arrived late at the stadium for the match and submitted its team sheet late.
Tottenham also faces charges "related to crowd disturbances" in Rome, UEFA said.
Like Lazio, Tottenham has advanced to the last 32 and will play Lyon, with the first leg at home on Feb. 14.
Lazio's hard-core "ultra" fans are known for their extreme right wing political views.