Ulissi held off Luxembourg's Jungels and Costa Rican Andrey Amador, who lies second overall, as the trio sprinted in 13 seconds ahead of the chasing pack.
It was Italian Ulissi's second stage win after his success on day four.
Spain's Mikel Nieve was the best-placed of Team Sky's riders in 25th. Lead rider Mikel Landa withdrew on Tuesday.
Giant-Alpecin's Tom Dumoulin, who won the opening time trial and wore the pink jersey for six days, dropped out of the race midway through Wednesday's stage because of saddle sores.
Stage 11 result:
1.  Diego Ulissi (Ita/Lampre) 4hrs 56mins 32secs
2.  Andrey Amador (Crc/Movistar) Same time
3.  Bob Jungels (Lux/Etixx-Quick-Step)
4.  Giacomo Nizzolo (Ita/Trek)  +13secs
5.  Sonny Colbrelli (Ita/Bardiani Valvole) Same time
6.  Matteo Trentin (Ita/Etixx-Quick-Step)
Overall standings:
1.  Bob Jungels (Lux/Etixx - Quick-Step) 45hrs 16mins 20secs
2.  Andrey Amador (Crc/Movistar) +26secs
3.  Alejandro Valverde (Spa/Movistar) +1min 7secs
4.  Steven Kruijswijk (Ned/LottoNL)  Same time
5.  Vincenzo Nibali (Ita/Astana) +1min 9secs
6.  Rafal Majka (Pol/Tinkoff)  +2mins 1sec
Bob Jungels retained the leader's pink jersey at the Giro d'Italia by keeping pace with a breakaway that gave Diego Ulissi victory on stage 11.