The Croatian champions have been fined €25,000 after their 1-0 win over CS Fola Esch, and had to close the east section of their stadium in Tuesday's clash against Sheriff
The chants occurred during the Croatian champions' victory over Luxembourg's CS Fola Esch in a Champions League second round qualifier on July 23.
Dinamo progressed and played Moldova's Sheriff Tiraspol in the Champions League third qualifying round on Tuesday but were ordered to close the east section of their stadium in a game they went on to win 1-0.
The club were charged by the Uefa Control and Disciplinary Body under the new Article 14 of the Disciplinary Regulations on racism, other discriminatory conduct and propaganda.
Uefa said on its website: "The fight against racism is a high priority for Uefa. Uefa has a policy of zero tolerance towards racism and discrimination on the pitch and in the stands.
"All forms of racist behaviour are considered as serious offences against the disciplinary regulations and are punished with the most severe sanctions."
It is another in a long list of racist incidents affecting European football at the moment, with AC Milan's Kevin Constant leaving the pitch earlier this month following racist chants aimed in his direction.