The Saxo-Tinkoff rider made a burst after the second Naso di Gatto climb was won by Colombian Julian Arrendondo Moreno, who maintained his grip on the King of the Mountains' blue jersey after a blistering first hour in which riders averaged 49kph.
The peloton tried to catch the 34-year-old Rogers as the 249km race powered towards its finish in Savona but he held off German Simon Geschke and Enrico Battaglin of Italy to capture his first ever individual Grand Tour stage win.
“It was definitely a beautiful moment. It was hard today for us. My team created an opportunity for me,” said Rogers, a three-times trial world champion and team captain at last year's Tour de France who was provisionally suspended in December.
He was able to ride again after the sport's governing International Cycling Union (UCI) ruled that he probably ate contaminated meat before testing positive for the banned substance clenbuterol last October.
“It was a spur of a the moment thing to attack," he added. "I saw at the top of the climb that the leaders of the general classification were sort of all looking at each other, and there was a possibility to go, so I took it.
Overall leader Cadel Evans of Australia retained his pink jersey by staying in the middle of the main peloton as the BMC Racing Team rider maintained a 57-second lead over Colombia's Rigoberto Uran of Omega Pharma-Quick-Step.
“The speed at the start, the middle and the climb added together to make it a really difficult stage,” said former Tour de France champion Evans.
There were only minor changes in the general classification but that is expected to change in Thursday's individual time trial stage over 41.9km from Barbaresco to Barolo in the Piedmont region which includes a series of tight turns.
“It's the first individual test and on paper it looks like a good time trial for me,” added Evans. “Like every time trial I hope to get everything down on the results sheet and see how that compares to the others in the general classification.”
(Reporting by Terry Daley; editing by Ken Ferris)
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