Inter fans taunted Spurs striker Emmanuel Adebayor and other black players with monkey chants, and the abuse was reported to UEFA by the match delegate and anti-discrimination body FARE.
The Italian club has also been charged with insufficient organisation and throwing of missiles and/or fireworks. The case will be dealt with on April 19.
UEFA said in a statement: "Proceedings [against Inter] have been opened on the following charges: racist behaviour of supporters, insufficient organisation, throwing of missiles and/or fireworks. The case will be dealt with on 19 April."
Inter look certain to escape with just a fine even if the charges are proved.
Piara Powar, executive director of European football's anti-discrimination body FARE, said it was the Italian club's first racism charge in Europe which under current UEFA rules means just a fine.
Inter have been sanctioned by the Italian FA this season - they were fined £43,000 for waving inflatable bananas and unfurling abusive banners aimed at Mario Balotelli and his team-mate Sulley Muntari in last month's Milan derby while the club also received a £12,900 fine after sections of their support sang racist chants about the former Manchester City striker during a game against Chievo.
Football Association chairman David Bernstein condemned the chants against Spurs and admitted the regularity of such abuse was worrying for the game.
He said last week: "I condemn the racist abuse that Tottenham Hotspur players suffered at last night's Europa League fixture in Milan.
"It is unacceptable and concerning that clubs in Europe have had to endure recurrences of abuse this season.
"I am sure UEFA will take appropriate action but it also reminds us of the need to work collectively across national and international football authorities to deal with this serious issue, as we are also doing in this country.
"This is a matter I will take up as a priority with the new FIFA anti-racism and discrimination task force when I meet its head Jeffrey Webb in the near future."