The Frenchman, who won Milano-Torino on Wednesday, whittled down a four-man lead group containing Vincenzo Nibali, Primoz Roglic and Egan Bernal to triumph on Lake Como.
Defending champion Nibali clung onto second, launching a brave attack in the closing stages just as he was about to be swallowed up. Dylan Teuns won the scrap for third.
‘A moment to savour’ – Pinot wins Il Lombardia
Martin opens up at Milano-Torino in preparation for Il Lombardia
The four-strong front group were each hoping to banish memories from a painful 2018, with Pinot suffering pneumonia at the Giro d’Italia, Nibali being wiped out by a fan’s camera strap at the Tour de France, Roglic crashing in the World Championships road race and Bernal only recently returning from a sickening fall at San Sebastian.
It was Pinot who proved the strongest, driving the tempo with 15 kilometres remaining as first Bernal, then Roglic and finally Nibali succumbed to the speed.
And the 28-year-old built on his advantage to claim the biggest win of his career by 32 seconds.
Romain Bardet wiped out by camera strap
T. Pinot5 hrs 53 mins 22 secs