Tinkoff-Saxo's Rogers, 34, rode clear of fellow escapee Francesco Bongiorno (Bardiani-CSF) after the Italian was involved in a controversial incident with an over-zealous spectator inside the closing three kilometres.
Another Italian, the veteran Franco Pellizotti (Androni-Giocattoli) went on to take second place on the stage, crossing the line of the snow-clad and spectator-covered Zoncolan 38 seconds after the impressive Rogers.
Bongiorno came home a further 11 seconds down, with Rogers' Tinkoff-Saxo team-mate Nicolas Roche - another rider from an initial 20-man break - taking fourth place at 1:35.
Colombia's Quintana, the maglia rosa from Movistar, finished 4:45 down on Rogers and alongside his compatriot Rigoberto Uran (Omega Pharma-Quick Step).
Quintana is one day away from being crowned the winner of the Giro d'Italia at his first attempt, with Uran - trailing by 3:07 on the general classification - in line to secure his second successive runner-up spot.
Italian Fabio Aru (Astana) finished in a group of other top ten riders to secure the third spot on the podium, 4:04 behind 24-year-old Quintana.
"It's amazing," said Rogers, the triple time trial world champion who also won stage 11 to Sestola. "It's always been an ambition of mine to win a mountaintop finish like that. The Zoncolan is a historic climb and it's an honour to win here.
"It's steep - one hell of a climb. The Zoncolan, Stelvio and Gavia are in the history of cycling. It's every child's dream to win here and I've done it."
Rogers' victory on what is largely considered the hardest ascent in professional climbing was not without incident, however.
With 2.5km remaining a fan attempting to push Bongiorno caused chaos when the 23-year-old clipped Rogers' wheel, swerved across the road and was forced to unclip to stay on his feet.
Seemingly unaware of the situation, Rogers rode on to open up a significant gap. Rattled by the well-intended but clearly poorly-executed intervention from the spectator, Bongiorno struggled to refind his rhythm and was eventually passed by Pellizotti in the final kilometre.
TWENTY-MAN BREAK: 20 riders formed a break off the front of the peloton shortly after the start of the 167km stage from Maniago. They were Axel Domont (Ag2R-La Mondiale), Franco Pellizotti and Jackson Rodriguez (both Androni Giocattoli), Francesco Bongiorno (Bardiani-CSF), Maarten Tjallingii (Belkin), Mattia Cattaneo (Lampre-Merida), Maxime Monfort (Lotto-Belisol), Yonathan Monsalve and Mattio Rabottini (both Neri Sottoli), Yukiya Arashiro (Europcar), Simon Geschke and Georg Preidler (both Giant-Shimano), Pieter Serry (Omega Pharma-Quick Step), Maxime Belkov (Katusha), Dario Cataldo (Sky), Michael Rogers and Nicolas Roche (both Tinkoff-Saxo), Danilo Hondo and Riccardo Zoidl (both Trek Factory Racing), and Brent Bookwalter (BMC).
Robinson Chalapud (Colombia) attacked the peloton on the first climb of the day, the Cat.1 Passo della Pura, over the summit of which Cataldo consolidated his second place in the blue jersey KOM competition. Tim Wellens (Lotto Belisol), Perriq Quemeneur (Europcar) and Edoardo Zardini (Badiani) joined Chalapud on the descent and the chasing group managed to bridge the gap on the second climb of the day, the Cat.2 Sella Razzo.
Meanwhile, the peloton rode more than six minutes in arrears - forcing the Europcar team of fourth-place Pierre Rolland to come to the front to lead the chase. Rolland tried to attack on the climb alongside Domenico Pozzovivo (Ag2R-La Mondiale) and Rafal Majka (Tinkoff-Saxo) but the main pack crossed the summit as one, 5:30 down on Cataldo, who has edged clear to take the points.
After a long 25km descent to the foot of the Zoncolan, the break stretched their advantage to just under eight minutes. This sparked a frenzy at the start of the final climb of the race, with the escapees all aware that they were most likely battling it out for the stage win. Rogers, Pellizotti and Bongiorno edged ahead with Preidler, Roche, Chalapud and Geschke before dropping their companions on the steepest 22% ramps of the fearsome climb.
Back with the main favourites, Igor Anton set a fierce pace for his Movistar leader Quintana, who soon found himself alongside Omega Pharma pair Uran and Wout Poels after the other GC favourites lost contact.
When Poels eventually succumbed to the laws of gravity and physics, it was left to the race's strongest two Colombian riders to ride shoulder to shoulder towards the finish line to cap what has been a remarkable race for the South American country.
BIG WINNER OF THE DAY: Mick Rogers started the season under a cloud of suspicion following the fall-out from his failed test for Clenbuterol last autumn. But once cleared, his season has gone from strength to strength. Only joining Tinkoff-Saxo's squad after a passport issue waylaid a team-mate, the Australian veteran has now snared two stages on his comeback tour - including the one everyone wanted to win: Monte Zoncolan.
BIG LOSER OF THE DAY: Cadel Evans (BMC) struggled on the steep mid-section of the climb and was the only rider to drop a place on GC, dropping to eighth at the expense of Dutchman Wilco Kelderman (Belkin).
KEY MOMENT: Who's to say what may have happened, but that over-aggressive push by the spectator clearly knocked the wind out of Francesco Bongiorno's sails - although the Italian youngster did look to be suffering after putting in an earlier out-of-the-saddle attack which came to nothing.
TALKING POINT: Are the Grand Tour organisers doing enough to control crowds on these 'epic' mountaintop finishes? The Bongiorno incident was the worst of a series of unsavoury incidents, with Wout Poels at one point forced to pull off the sunglasses of one fan and thrown then to the side of the road in disgust.
COMING UP: The final day of the 97th edition of the Giro features eight laps of a criterium-style circuit race in the Adriatic port of Trieste. Frenchman Nacer Bouhanni (FDJ) will look to secure the red points jersey and win his fourth scalp of the race - but he'll face stiff competition from the remaining sprinters in the race, such as Elia Viviani (Cannondale), Ben Swift (Sky), Luka Mezgec (Giant-Shimano) and Giacomo Nizzolo (Trek).
- Sports & Recreation
- Franco Pellizotti
- Francesco Bongiorno
- Nicolas Roche
- Rigoberto Uran
- Dario Cataldo
- Michael Rogers