Frankfurt, who lost the first leg 2-0 in Germany, expected just under 3,000 travelling fans in the stadium for the game.
"Eintracht Frankfurt were informed yesterday late evening from UEFA that Italy's interior ministry would issue a regulation today that bans the (Italian) club from selling tickets to fans of Eintracht Frankfurt for the return leg on March 15," the German club said in a statement.
"This shall include the entire visiting fan contingent of 2,700 including 2,400 in the visiting fans sector, that Eintracht were eligible for.
"Frankfurt will comment further on this development once there are specific details of the regulation available."
Fans of both teams clashed prior to the first leg in Frankfurt with police having labelled that game as high risk.
Europa League winners last year, Frankfurt, are enjoying their best run in decades on the pitch with fans offering strong support in away matches.
Tens of thousands of Eintracht fans travelled to Seville for that final with the club having had just 10,000 tickets at their disposal.
