Omega Pharma-Quick Step's Uran beat double stage winner Diego Ulissi (Lampre-Merida) by a huge one minute and 17 seconds as he set a blistering time of 57:34 over the highly technical and undulating 41.9km course through the vineyards of the rolling Langhe hills.
Veteran Australian Evans (BMC) came home in third place, 1:34 down on Uran, to concede the maglia rosa to the Colombian. Uran, 27, now holds a 37-second gap over Evans at the top of the GC.
"I'm surprised. I was doing a great time trial but I didn't think I'd win it," said Uran, who became the first Colombian in history to wear the pink jersey.
Uran was one of four riders from Omega Pharma-Quick Step to finish in the top ten, with Gianluca Brambilla (fifth), Wouter Poels (sixth) and Thomas De Gendt (eighth) all starring.
"With Specialized I've been doing a lot of work over the winter," Uran admitted. "I was fourth in the Tour of Romandie ITT and so that was a good sign. I'm lost for words - it's incredible."
Heavy rain and thunderstorms thwarted the early starters of the race's first individual time trail, making the tight bends of two lengthy descents rather treacherous.
Sweden's Tobias Ludvigsson - who had set the fourth best time at the first check in Boscasso after 12.6km - lost control on a sweeping bend before flying over a road barrier and landing heavily in a driveway. The Giant-Shimano rider was taken to hospital and forced out of the race.
It was in such testing conditions that Belgium's De Gendt set a landmark time which remained unbeaten until Ulissi surprised with his stellar effort.
With the rain easing up and the roads drying, the late starter had a slight advantage - and Domenico Pozzovivo (Ag2R-La Mondiale) was quickest up the first climb to set a target time in Boscasso that would not be beaten.
Uran, 15 seconds down on Pozzovivo at the first check, rode the downhill segment to Alba with perfection, moving 27 seconds above Ulissi's target time in the truffle capital of Italy.
Evans crossed the second intermediate check after 26.2km 59 seconds in arrears - making Uran the virtual pink jersey by two slender seconds.
Pozzovivo faded on the second half of the course and Ulissi's time in Barolo was not threatened until the arrival of the young Polish rider Rafal Majka (Tinkoff-Saxo).
Wearing the white jersey as best young rider of the race, Majka crossed the line 22 seconds down on Ulissi with just two more riders - Uran and Evans - left to arrive.
Watching in the finish area, Ulissi could only applaud and doff his cap as Uran zipped up the final climb into the famous wine town of Barolo to beat the young Italian quite emphatically.
It was then a question of damage limitation for Evans who rallied to post the third best time but lose the famous maglia rosa.
Majka finished the stage in fourth place to stay in third place on GC, 1:52 down on Uran. Pozzovivo is fourth after fading to finish 2:09 down on Uran in ninth place in Barolo.
Dutch youngster Wilco Kelderman (Belkin) rode to a solid seventh place to move up to fifth on GC, 2:50 in arrears. Meanwhile, the pre-race favourite Nairo Quintana (Movistar) finished outside the top ten but rose to sixth on GC, a huge 3:29 behind his fellow Colombian.
BIG WINNER OF THE DAY: Rigoberto Uran became the first Colombian to don the Giro's maglia rosa. Riders from three different continents have now worn the pink jersey - but no one, as yet, from Europe.
BIG LOSER OF THE DAY: Italian veteran Ivan Basso (Cannondale) crashed with 4km to go and dropped out of the top ten.
KEY MOMENT: As soon as Uran posted the best time at the second intermediate check in Alba to confirm his blistering opening segment it became clear that we were watching something very special.
TALKING POINT: Can Nairo Quintana still win this Giro d'Italia? Thursday's ITT was always going to be a question of damage limitation, but the Colombian will enter the Alps with more than three minutes to claw back on his compatriot Uran.
COMING UP: The transitional 157km stage 13 from Fossano to Rivarolo Canavese spirits the riders towards the foot of the Alps and should provide the sprinters with a final chance to compete for honours ahead of the Alpine showdown over the weekend.
- Sports & Recreation
- Diego Ulissi
- Rigoberto Uran