Rijeka had one-goal advantage from the first leg. Ivan Tomečak secured the 1:0 away win at Maksimir last Wednesday.
In the 35th minute of the return leg, the hosts took the lead when Mitrović headed home after a corner kick.
Ten minutes before the end, Jugović found Kvržić in the box, and Kvržić found the net to mark the beginning of the celebrations at the packed Kantrida stadium.
Rijeka won the Croatian Cup for the third time in history, after winning two consecutive title in 2005 and 2006.
The gold medals and the trophy were presented by the Croatian Football Federation president Davor Šuker and Rijeka president Damir Mišković.
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