The BMC rider kept his powder dry in the slippery and wet conditions and waited until the final 500 meters before launching his winning attack. He finished three seconds ahead of race leader Alberto Contador (Tinkoff-Saxo) and Diego Ulissi (Lampre-Merida).
"The team did a great work today. Yesterday too we worked but the stage was too hard for me, and I was frightened of losing my team-mate's confidence," Gilbert said.
"But at our meeting before the stage we decided to give it everything today. I came to look at this stage after Milan-San Remo, and I knew every detail of the final 70km. Fabio Baldato was in the team car, giving encouragement and information.
"The finish was very hard, and the weather was horrible, not cold, but wet, but the final 400m went perfectly. It’s a great feeling."
Contador managed to extend his lead on a struggling Fabio Aru and now leads the Astana rider by 17 seconds on the general classification. Mikel Landa (Astana) sits in third place at 55 seconds.
Australia's Richie Porte (Sky) also lost a small amount of time to Contador in the charge to the finish but appeared to be riding to stay safe ahead of the Stage 14 time trial where he is expected to regain a substantial amount of time lost to his rivals.
With its flat start from Imola, the 190km stage progressed as expected, with Patrick Gretsch (AG2R), Davide Appollonio (Androni-Giocattoli), Enrico Barbin (Bariani-CSF), Kenny Elissonde (FDJ) and Nick Van der Lijke (LottoNL-Jumbo) leading the race for the first 130km.
The five-rider exploit ended on the category four Castelnuovo climb as the peloton came together for the final 60km of racing, with a series of similarly categorised bumps ahead of a punchy uphill finish in Vicenza.
The stage turned on the Crosara as the rain and riders came down in the increasingly treacherous conditions. Orica-GreenEDGE went into the stage with Simon Gerrans as their leader but he slid out of contention on the winding descent, leaving team-mate Michael Matthews to fly the flag for Australia.
Yet the conditions did nothing to stop the leading riders who stayed together to the end. Attacks were launched by several riders but all failed in the conditions and the final gradient forced the winning selection led by Gilbert, Contador and Ulissi.
"It was another very hard day. We rode the first two hours at about 50 kph, then the rain started," Contador said. The peloton broke apart with the high speeds, but I had good legs.
"Philippe Gilbert was very strong on the final climb, but I was thinking of the general classification and I’m very happy with the outcome today."
Stage 12: 190km, Imola - Vicenza
1 Philippe Gilbert (BEL) BMC 4hr 22min 50sec
2 Alberto Contador (ESP) Tinkoff-Saxo 0:00:03
3 Diego Ulissi (ITA) Lampre-Merida
4 Simon Geschke (GER) Giant-Alpecin
5 Enrico Battaglin (ITA) Bardiani CSF
6 Paolo Tiralongo (ITA) Astana
7 Ion Izagirre (ESP) Movistar 0:00:06
8 Carlos Betancur (COL) AG2R
9 Jurgen Van Den Broeck (BEL) Lotto-Soudal
10 Mikel Landa Meana (ESP) Astana
1 Alberto Contador (ESP) Tinkoff-Saxo 51hr 17min 6sec
2 Fabio Aru (ITA) Astana 0:00:17
3 Mikel Landa Meana (ESP) Astana 0:00:55
4 Dario Cataldo (ITA) Astana 0:01:30
5 Roman Kreuziger (CZE) Tinkoff-Saxo 0:01:55
6 Rigoberto Uran (COL) Etixx-QuickStep 0:02:19
7 Giovanni Visconti (ITA) Movistar 0:02:21
8 Damiano Caruso (ITA) BMC 0:02:29
9 Andrey Amador (CRC) Movistar 0:02:38
10 Leopold Konig (CZE) Sky 0:02:44
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