Ulissi (Lampre) won the 227-kilometre route from Modena to Asolo, with Luxembourg’s Jungels (Etixx-QuickStep) third.
Jungels’ lead was trimmed as Costa Rica’s Andrey Amador (Movistar) claimed crucial bonus seconds by finishing second to Ulissi, who also won stage four. Jungels leads Amador by 24 seconds entering Thursday’s 182km stage from Noale to Bibione.
Italy’s Vincenzo Nibali (Astana) finished 21st, 13 seconds behind and one place ahead of Canada’s Ryder Hesjedal (Trek-Segafredo), the 2012 winner.
Ulissi made a late attack to take victory, as Jungels settled for finishing ahead of the overall favourites.
Jungels said: “When I saw the opportunity to get away from the group of favourites, I made my move.
“At the end I tried to gain as many seconds as I could in order to keep the maglia rosa as long as I can.”
Tom Dumoulin (Giant-Alpecin) abandoned during the 11th stage, following complications with saddle sores.
The Dutchman won the opening stage in Apeldoorn, Holland to take the first pink jersey of the race.
1. Diego Ulissi (Ita) Lampre-Merida, in 4-56-32 2. Andrey Amador (CRC) Movistar 3. Bob Jungels (Lux) Etixx-Quick Step, all same time 4. Giacomo Nizzolo (Ita) Trek-Segafredo, at 13s 5. Sonny Colbrelli (Ita) Bardiani-CSF 6. Matteo Trentin (Ita) Etixx-Quick Step 7. Sacha Modolo (Ita) Lampre-Merida 8. Enrico Battaglin (Ita) LottoNL-Jumbo 9. Tim Wellens (Bel) Lotto-Soudal 10. Alejandro Valverde (Esp) Movistar, all same time
Selected others 102. Nicolas Roche (Irl) Team Sky 11 mins 56 secs 104. Phillip Deignan (Irl) Team Sky same time
Overall classification after stage 11 1. Bob Jungels (Lux) Etixx-Quick Step, in 45-16-20 2. Andrey Amador (CRC) Movistar, at 24s 3. Alejandro Valverde (Esp) Movistar, at 1-07 4. Steven Kruijswijk (Ned) LottoNL-Jumbo, st 5. Vincenzo Nibali (Ita) Astana, at 1-09 6. Rafal Majka (Pol) Tinkoff, at 2-01 7. Ilnur Zakarin (Rus) Katusha, at 2-25 8. Esteban Chaves (Col) Orica-GreenEdge, at 2-43 9. Gianluca Brambilla (Ita) Etixx-Quick Step, at 2-45 10. Diego Ulissi (Ita) Lampre-Merida, at 2-47
31 Roche at 21 mins. 115 Deignan at 1 hour 18 mins 37 secs