The Australian rode away from the peloton near the bottom of the final climb of Paracombe, and held off chasers Gorka Izagirre (Movistar) and Esteban Chaves (Orica-Scott) to win alone by 16 seconds.
Caleb Ewan went into the day as the race leader after his victory on the opening stage but put his personal ambitions aside to help his teammates and ended up losing almost 10 minutes in the overall standings.
With the bonus second at the top of the climb, Porte now holds a 20-second lead over Izagirre and a further two seconds on Chaves.
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