It was Wawrinka's third title of 2016 and first on clay just a day before Roland Garros gets underway in Paris.
World number four and top seed Wawrinka broke the 11th-ranked Cilic to take a 2-1 lead on his way to the first set.
Cilic hit back for a 4-1 advantage in the second set before 31-year-old Wawrinka broke the Croat at 3-5 to get the second set back on serve.
In the tie-break, Cilic squandered five set points before Wawrinka took victory on his second match point.