The Croatian champions were also fined 20,000 euros (17,135.88 pounds)while an on order to play a second game behind closed doors was deferred for a probationary period of two years.
The club were fined a further 47,000 euros for the setting off of fireworks and throwing of objects by fans and for blocked stairways.
Zagreb won the Europa League round-of-16 home match 1-0 but were beaten 3-0 after extra-time in the return in Lisbon and eliminated.
Dynamo Kiev were ordered to close part of their stadium for their next home European game following a pitch invasion in the match at home to Olympiakos in February. UEFA said fans also set off fireworks and threw missiles.
Malmo and Chelsea were fined 58,000 euros and 13,000 euros respectively following incidents at their round of 32 match in February.
(Reporting by Brian Homewood, editing by Ed Osmond)
