The Katusha rider, who recently won the Tour de Romandie, attacked his breakaway companions with 23km to go to ride away with the stage victory on the Imola Autodrome.
Despite race leader Alberto Contador attacking on the final climb, he could not distance any of his rivals.
Fabio Aru (Astana) could not immediately respond when the Maglia Rosa made his move 150m from the top of the Tre Monti, but the peloton brought back the Spaniard to keep the general classification at status quo. Contador holds a three second lead over Aru, with his team-mate Mikel Landa 46 seconds back. Richie Porte is 12th, 3min 9sec back after receiving a two-minute penalty on Stage 10 for taking a wheel from Orica-GreenEDGE's Simon Clarke when he punctured.
“The terrain wasn’t ideal for an attack, but sometimes you just go on instinct: it depends on whether you feel good or not. Today was very hard, much harder than yesterday, with 50km less. I’m feeling better each day, and the bruising on my legs is getting better. A thousand things can still happen. It may look easy, but there is still a very long way to go.” - Alberto Contador
After the controversy of Stage 10 of the Giro d’Italia, Stage 11 was a much more subdued affair with a lumpy 153km from Forli to Imola. The race split on the first climb of the day, the Passo del Trebbio, with a group of 11 riders holding a 15 second advantage on the peloton over the summit of the climb.
The group - Carlos Betancur, Matteo Montaguti (Ag2r La Mondiale), Franco Pellizotti (Androni - Sidermec), Diego Rosa (Astana), Marek Rutkiewicz (CCC Sprandi), Beñat Intxausti (Movistar), Ruben Fernandez (Movistar), Ryder Hesjedal (Cannondale - Garmin), Ilnur Zakarin (Katusha) and Steven Kruijswijk (LottoNL - Jumbo) - steadily increased their lead until they had over three minutes with 80km to go.
It was BMC Racing who were present at the front of the peloton, hoping the stage could be one for former world champion Philippe Gilbert.
The race culminated with four laps of a 15km circuit which took in part of the Imola Grand Prix course and featured the four kilometre long Tre Monti climb.
As the kilometers dipped below 50km to go the breakaway clung to a 1min 18sec lead. Their advantage shrunk to just 43 seconds with 43km to go before the diminshed peloton eased off to allow them to draw it back out to a minute and a half on the second lap .
Individual pursuit world champion Stefan Kung (BMC) attacked and went solo in no man’s land, forcing Orica-GreenEDGE to make their way to the front of the peloton with 30km to go. Kung’s move came to nought by the time the race hit the penultimate lap.
Zakarin attacked his six remaining breakaway companions midway up the climb with 23km to go. Former Giro winner Hesjedal put in a major effort in the chase but received no assistance, meaning it was the last they would see of the 25-year-old Russian.
Further back, the wet and slippery roads were splintering the peloton, with Etixx-Quick-Step leader Rigoberto Uran crashing. However the Colombian was quick to return to the front of the peloton, which was still lead by Orica-GreenEDGE.
As Zakarin crested the climb for the final time he held a 1min 50sec gap on the peloton. With only eight kilometres remaining, the victory was certain to be his.
“I started the stage in good heart, and the breakaway riders worked well together. I made one attempt to get away, and at the second try, I made it. I learned a lesson in the stage that Intxausti won because that day I made the mistake of attacking too early. This time, I waited until the last moment. I still can’t believe that I won the Tour de Romandie, and now I’ve won a stage of the Giro. I have many emotions, and I’m very happy.” - Ilnur Zakarin
The young rider is in his first year in the WorldTour with Katusha. In 2009 he faced a two-year ban after testing positive for the anabolic steroid methandienone. On his return to racing he spent some time in the Professional Continental ranks with RusVelo before joining Katusha this season.
Stage 11: 153km, Forli - Imola
1 Ilnur Zakarin (RUS) Team Katusha 3hr 55min 08sec
2 Carlos Betancur (COL) AG2R La Mondiale 0:00:53
3 Franco Pellizotti (ITA) Androni Giocattoli
4 Benat Intxausti (ESP) Movistar
5 Diego Rosa (ITA) Astana
6 Steven Kruijswijk (NED) LottoNL-Jumbo
7 Ryder Hesjedal (CAN) Cannondale-Garmin
8 Maciej Paterski (POL) CCC Sprandi Polkowice 0:00:58
9 Philippe Gilbert (BEL) BMC Racing
10 Juan Jose Lobato (ESP) Movistar 0:01:02
1 Alberto Contador (ESP) Tinkoff-Saxo 46hr 54min 19sec
2 Fabio Aru (ITA) Astana 0:00:03
3 Mikel Landa Meana (ESP) Astana 0:00:46
4 Dario Cataldo (ITA) Astana0:01:16
5 Roman Kreuziger (CZE) Tinkoff-Saxo 0:01:46
6 Rigoberto Uran (COL) Etixx-Quick-Step 0:02:10
7 Giovanni Visconti (ITA) Movistar 0:02:12
8 Damiano Caruso (ITA) BMC Racing 0:02:20
9 Andrey Amador (CRC) Movistar 0:02:24
10 Leopold Konig (CZE) Sky 0:02:30