The Bahrain-Merida rider, who also won the race in 2015, dropped Frenchman Thibaut Pinot in the descent from the Civiglio hill and never looked back.
He crossed the finish line 28 seconds ahead of France's Julian Alaphilippe, according to the provisional results. Another Italian, Gianni Moscon, took third place after the 247km ride from Bergamo.
"Il Lombardia" is the last of five Monument (top) one-day classics in the season after Milan-San Remo, Paris-Roubaix, the Tour of Flanders and Liege-Bastogne-Liege.
"The idea was to do basically what I did two years ago with an attack in the descent," said Nibali.
Belgian Laurens De Plus crashed into a ravine on a downhill but escaped with "no serious injuries", his Quick-Step Floors team said.
Pinot, of the FDJ team, was on the attack in the climb to Civiglio. The Frenchman, fourth overall in the Giro d'Italia this year, accelerated three times and only Nibali could follow.
The duo were together at the top but the Italian lived up to his reputation as the best descender in the world to open an unassailable gap.
Pinot then faded and took fifth place. His compatriot Alexis Vuillermoz had been demoted for an alleged foul in the final sprint but was later reinstated.
"I've got no regret. I raced to win. I was not interested in just finishing on the podium," said Pinot.
(This version of the story was officially corrected to make clear Pinot is fifth after Vuillermoz was reinstated into fourth place)
(Writing by Julien Pretot; Editing by Ed Osmond, Neville Dalton)
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