The match, which finished goalless, was suspended for two minutes shortly after the half-time interval by referee Gianluca Rocchi, allowing the stadium announcer to order offenders to desist before play was allowed to resume.
Rocchi was using a procedure introduced in the wake of Milan midfielder Kevin-Prince Boateng's decision to lead his team-mates off the pitch during a friendly game at Pro Patria in January, forcing the abandonment of the match and sparking new debate on the subject of racism in Italian football.
Although the Lega did not specify which three players it believed had been targeted by Roma fans, striker Mario Balotelli was seen raising his finger to his lips in a bid to silence visiting fans.
Roma captain Francesco Totti then approached the away end at San Siro during the suspension to reason with offending Giallorossi supporters.
A statement published on legaserie.it read: "A fine of 50,000 euros with a warning for Roma, whose supporters continuously addressed racially discriminatory chants to three players of the opposing team, prompting the referee to suspend the game for two minutes in order to make them desist from such reprehensible behaviour."