Ulissi (Lampre-Merida) finished ahead of Julian Arredondo (Trek Factory Racing) and Australia’s Cadel Evans (BMC) at the end of the 203km stage from Taranto.
Race leader Michael Matthews (Orica-GreenEDGE) rode strongly to finish with the leaders and hold his position on the general classification ahead of team-mate Pieter Weening and Evans, who leapfrogged Rigoberto Uran (Omega Pharma-Quick-Step) into third place after time bonuses were factored in.
"I really liked the course, the final climb was suitable for high tempo and for a late move," said an elated Ulissi. "Everyone said I was one of the favourites; and yes it's good that my qualities are receiving attention, but it's also not so easy to fulfill those expectations.
"When I attacked, it was with everything, and very late. It was the right time. I'm delighted."
Earlier in the stage an 11-rider break which included Elia Viviani (Cannondale), Ben Swift (Sky) and Tyler Farrar (Garmin-Sharp) rode out to a lead of five minutes before the chasers warmed up.
With Matthews in the Maglia Rosa, Orica-GreenEDGE did the work at the front of the peloton, helping to eat away at the lead of the break as it captured the spoils of the intermediate sprint and points on the Valico di Serra san Chirico climb.
Giro d'Italia stage 5 highlights
The pattern continued all the way to the 14km mark where the last of the breakaway riders were caught and more teams took their turn sharing the work with two category four climbs sandwiching a tricky descent on the finishing menu.
As the first of the two climbs in Viggiano began to bite, the peloton split into several groups as the BMC team of Cadel Evans upped the tempo in wet conditions.
The slippery descent shook several riders off their bikes while Gianluca Brambilla (Omega Pharma-QuickStep) took a long range chance for victory.
Brambilla carried his lead up the kilometre mark before he was shut down by Katusha and contenders for the stag win strained for an advantage.
But is was Ulissi who had saved his best for last with an unmatched acceleration which he carried to the finish as Evans and Arredondo chased.
Overall contenders come out to play
Cadel Evans (BMC) took third in the uphill sprint to establish himself as a strong contender, while Rigoberto Uran (OPQS), Joaquim Rodriguez (Katusha), and Nairo Quintana (Movistar) were all present and accounted for. Evans, who moved into third overall off the result, said the stage had been encouraging, but the Giro still had a long way to go.
"l am happy about the result," the Australian said, "The finish wasn't perfect for me, but the way I performed today is confirmation that I am in good form, and that is very satisfying."
Meanwhile Matthews, who saved the pink jersey, and is set to wear it for a fifth straight day for Stage 6 says he was disappointed to miss out on the stage win, but overwhelmed at the prospect of keeping the lead as long as he has.
"The goal for the day was the stage win, but to keep the jersey is also a huge thing," Matthews said. "If you watched the race today, you saw the boys riding on the front for the entire race.
"Any of them could be in the jersey right now. I’m just the lucky one that has it on my back. I would have liked to win the stage to pay them back for all the work they’ve been doing for me these last couple days."
Thursday's sixth stage is one of the longest of the race at 257km from Sassano to Montecassino, with the closing stages a 8.7km climb. The stage will be live on SBS from 2300.
Stage 5: 203km, Taranto to Viggiano
1 Diego Ulissi (ITA) Lampre-Merida 5hr 12min 39sec
2 Julian Arredondo (COL) Trek Factory Racing 0:00:01
3 Cadel Evans (AUS) BMC
4 Rigoberto Uran (COL) Omega Pharma-QuickStep
5 Rafal Majka (POL) Tinkoff-Saxo
6 Michael Matthews (AUS) Orica-GreenEDGE
7 Joaquin Rodriguez (ESP) Katusha
8 Wilco Kelderman (NED) Belkin
9 Domenico Pozzovivo (ITA) AG2R
10 Nairo Quintana (COL) Movistar
General classification
1 Michael Matthews (AUS) Orica-GreenEDGE 17hr 41min 23sec
2 Pieter Weening (NED) Orica-GreenEDGE 0:00:14
3 Cadel Evans (AUS) BMC 0:00:15
4 Rigoberto Uran (COL) Omega Pharma-QuickStep 0:00:19
5 Rafal Majka (POL) Tinkoff-Saxo 0:00:26
6 Edvald Boasson Hagen (NOR) Sky 0:00:35
7 Nicolas Roche (IRL) Tinkoff-Saxo 0:00:37
8 Michele Scarponi (ITA) Astana 0:00:41
9 Dario Cataldo (ITA) Sky 0:00:49
10 Fabio Aru (ITA) Astana 0:00:52
SBS will broadcast every stage of the 2014 Giro d'Italia LIVE! There will be nightly highlights at 5:30pm on SBS ONE, and each stage will also be streamed live here at Cycling Central.
SBS will broadcast every stage of the 2014 Giro d'Italia LIVE! There will be nightly highlights at 5:30pm on SBS ONE, and each stage will also be streamed live here at Cycling Central.
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