The Lampre rider was never threatened and finished in a 21-man leading pack in a 181km stage won in a sprint by Italy's Andrea Guardini (Farnese Vini) from countrymen Jacopo Guarnieri (Liquigas) and Alessandro Petacchi (Lampre).
The 21-year-old Ulissi claimed the overall lead after his stage win on Saturday, and completed his second career victory after 2010's Gran Premio Industria e Commercio di Prato. He also won stage 17 of this year's Giro d'Italia.
He finished comfortably clear of Radoslav Rogina (Loborika Favorit) with home rider Robert Vrecer (Perutnina Ptuj) completing the podium.
Another Slovenian, Kristijan Koren (Liquigas) won the sprinters' points classification.