Cannondale-Garmin rider Formolo, 22, soloed clear of a 14-man break ahead of the third and final categorised climb of the 150km stage in Luguria before securing a first professional win in the coastal town of La Spezia.
Formolo finished 22 seconds clear of Clarke, who took over the race lead from Orica-GreenEdge team-mate Michael Matthews.
Matthews was one of many riders blown away from some devastating riding from the Astana team of Fabio Aru. The Italian youngster – third in last year’s Giro - attacked from the streamlined peloton on the final climb, taking rivals Alberto Contador (Tinkoff-Saxo) and Richie Porte (Team Sky) with him.
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Aru, Contador and Porte all finished in the Clarke chasing group to set the scene perfectly ahead of the race's first mountain top finish in Abetone on Wednesday.
Clarke now leads team-mate Esteban Chaves by 10 seconds on the general classification after the Colombian also finished in that main chasing group to complete another impressive display by Orica-GreenEdge, who have held the maglia rosa since the opening time trial on Saturday.
Roman Kreuziger – also part of the day’s main break – is in third place 17 seconds in arrears alongside team-mate Contador, with Aru rising to fifth place at 23 seconds.
Among the big losers of the day was Colombia’s Rigoberto Uran, who not only conceded valuable seconds on the race’s big trio but also lost a second Etixx-QuickStep team-mate after Gianni Meersman was forced to retire following injuries sustained during a crash on Monday.
PULSATING START: Although just the fourth of 21 stages, it was a day of plots and subplots aplenty as the race was animated by an early break of 30 riders going clear.
Astana (Dario Cataldo, Andrey Zeits), Team Sky (Kanstantin Siutsou, Salvatore Puccio), Orica-GreenEdge (Clarke, Chaves), Movistar (Andrey Amador, Giovanni Visconti), Cannondale-Garmin (Formolo, Tom Danielson), Bardiani-CSF (Edoardo Zardini, Sonny Colbrelli) and BMC (Amael Moinard, Darwin Atapuma) all had two riders each ahead of the pack, but it was the presence of Tinkoff-Saxo’s Roman Kreuziger that raised eyebrows.
With the advantage over the pack pushing 10 minutes after the first of three categorised climbs, Kreuziger – along with Clarke and Chaves – looked set to snare the pink jersey, regardless of the outcome of the stage.
The composition of the leading faction changed throughout the opening half of the stage, with groups and chasing groups forming and coming together. With just over 80km remaining – on a series of hills ahead of the second categorised climb of the day – 28 riders finally came together with around nine minutes to play with over the pack.
With the gap coming down to eight minutes at the feedzone in the coastal town of Levanto with 55km remaining, the victor looked all but certain to be one of the escapees. And while that indeed turned out to be the case, no one could have predicted what was about to happen.
ASTANA DRAMA: Six riders came together on the front of the race on the Cat.3 Passo del Termine, with Puccio, Moinard and Formolo catching the leading trio of Zeits, Colbrelli and Moinard.
The remaining escapees rode 30 seconds down the road just as Astana decided to wrest control of the peloton from the Tinkoff-Saxo and Etixx team-mates of Contador and Uran.
Setting an infernal pace, Astana had slashed the gap to less than six minutes as Matthews, the race leader, joined numerous riders in a gruppetto off the back of the race.
With Kreuziger up the road in the chasing group, Contador soon found himself isolated with only Australian veteran Mick Rogers for support. Porte had two team-mates while Aru revelled alongside five Astana team-mates, knowing that both Zeits and Cataldo could be called on if necessary.
A series of fast straights and zippy descents as the road headed towards La Spezia saw Astana grab the race by its neck, reducing the peloton to just about 30 riders and cutting the lead to just two minutes for the escapees, who had reformed a 15-man group ahead of the 17km finish circuit.
FORMOLO & ARU ATTACK: Making light of his inexperience, second-year pro Formolo attacked his fellow escapees just ahead of the third categorised climb with 13km remaining. Visconti and Moinard combined in pursuit as the remaining leaders cancelled each other out.
Now only a minute behind, the main pack – or what was left of it – was blown apart when Aru unleashed a stinging attack to which only Contador and Porte had an answer.
The trio of race favourites soon caught the remnants of the break before Formolo crossed the summit at Biassa with a 30-second lead over Visconti and Moinard. The newly invigorated chasing group passed 20 seconds later to set up a tense final 10km.
The cherubic Formolo kept his cool on the descent and was a picture of happiness when he punched the air to secure a stage win in his first appearance in the Giro.
CLARKE GAFFE: Twenty-two seconds later, Clarke won the sprint for second place – but by the look of his elaborate celebrations, the Orica-GreenEdge rider clearly believed he had just added a Giro win to his Vuelta scalp from 2012.
But his raised arms and bellowing cry were not for nothing: Clarke’s finish ensured he would be the third Australian rider from Orica-GreenEdge to wear the pink jersey since Simon Gerrans took the race lead after Saturday’s opening stage in San Remo.
"You saw the emotion crossing the line – I was just stoked to keep the jersey in the team,” Clarke said after his appearance on the podium, somewhat downplaying his mistake.
Contador, Aru and Porte all finished in the same group, with Porte claiming he stage was "the hardest of the race so far”. The Tasmanian – now 37 seconds down on GC in 10th place – singled out rival Aru’s team for their performance, admitting that "Astana were absolutely incredible today. Without them the race might have already been lost.”
Runner-up for the past two years, Uran finished in a second chasing group 42 seconds down on his GC rivals to cap another miserable day for Etixx-QuickStep. The Colombian is now 14th on GC at 1:11.
Other casualties of a brutal day in the saddle included Spain’s Benat Intxausti of Movistar, who lost over nine minutes, and Tour of Romandie winner Ilnur Zacharin (Katusha), who shipped over 17 minutes. Overnight leader Matthews came home in the gruppetto 20 minutes down on the man of the moment, Formolo.
Wednesday’s first foray into the mountains sees the race enter Tuscany with a 152km ride that finishes in the Apennine ski resort of Abetone.
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