The start of the second half was delayed after City returned to the Jose Alvalade Stadium pitch about a minute late.
City lost the first leg of the round of 16 fixture 1-0 and went out on away goals after only winning the second leg 3-2.
The fine is more than the €20,000 ($26,300) FC Porto received after its fans aimed racist abuse at Manchester City players during a Europa League match in February. Mario Balotelli and Yaya Toure, who are both black, reported hearing abusive chants.
English football's anti-racism group said City's fine was out of proportion compared with the punishment for the racism at Porto.
"This fine (for City) does nothing to help UEFA's reputation in relation to how it tackles discrimination in football," said Herman Ouseley, chairman of Kick It Out. "We've seen significant punishments meted out in the past but, as an organization, the line it takes on such matters has lacked consistency.
"With the European Championship looming (in Poland and Ukraine), and the potential flashpoints which may occur during the tournament with right-wing groups in eastern Europe, this seems to conflict with the strong anti-racism message UEFA should be promoting."
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