The 41-year-old refereed the Champions League final in May which saw Chelsea beat Bayern Munich on penalties.
Proenca's compatriots Bertino Cunha Miranda and Ricardo Jorge Ferreira Santos will run the lines in Kiev on Sunday, while Manuel Jorge Neves Moreira De Sousa and Duarte Nuno Pereira Gomes will be additional assistant referees.
Proenca and his team have already overseen Spain's 4-0 Group C win over the Republic of Ireland and Sweden's 2-0 victory against France in Group D.
They were also in charge at the England-Italy quarter-final, which the Azzurri won 4-2 on penalties after a goalless 120 minutes.
UEFA said that Proenca had been "on the rise in European refereeing circles" since officiating the European under-19 championship final in 2004.
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