The 41-year-old also officiated in the Champions League final, won by Real Madrid over city rivals Atletico in May.
He becomes the second man to take charge of both major European occasions in the same year after Pedro Proenca of Portugal in 2012, UEFA said in a statement.
Clattenburg was also the referee for the FA Cup final won by Manchester United over Crystal Palace in May, after which Palace manager Alan Pardew said he was frustrated by two of his decisions.
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Sunday's final will be Clattenburg's fourth appointment at the finals following Belgium v Italy, Czech Republic v Croatia and Switzerland v Poland. He was also a fourth official when Iceland played Austria.
(Reporting by Patrick Vignal; editing by Sudipto Ganguly)
