Cold, wet and snowy conditions led to the decision to shorten the stage as two high-altitude climbs at the Fedaia and Pordoi passes were cut from the race.
But the Ineos Grenadiers rider battled against the elements to finish 27 seconds ahead of Frenchman Romain Bardet and Italy's Damiano Caruso.
"I wanted to put on a show. This is the kind of cycling I like, when it's wet and cold and you need grit," Bernal said.
"I wanted to do something special. It's risky but I thought I could do it, and the team believed in me."
Bernal now has a lead of two minutes and 24 seconds over second-placed Caruso in the general classification rankings.
British Maglia Rosa hopeful Simon Yates lost two minutes and 36 seconds on Bernal in the Dolomites, finishing 11th in the stage to fall from second to fifth overall, four minutes and 20 seconds behind the Colombian.
Bernal now has a lead of two minutes and 24 seconds over second-placed Caruso in the general classification rankings.
Britain's Hugh Carthy and Russia's Aleksandr Vlasov are third and fourth, with gaps of three minutes 40 seconds and four minutes 18 seconds respectively.
The poor weather also impacted the television coverage, as the aircraft that transmits the signal was unable to take off and camera helicopters could not fly.
Bernal's descent from the 2,236-metre summit of the Passo Giau - the highest point in the Giro - to the finish line therefore went unseen by those watching from afar.
The 24-year-old surged past Antonio Pedrero to take the lead with 21 kilometres to go and by the time he appeared in Cortina d'Ampezzo he was all alone.
He even took the time to remove his rain jacket and show off the leader's pink jersey before crossing the finish line.
There is a rest day on Tuesday before stage 17 on Wednesday, a 193km ride from Canazei to Sega di Ala.
WATCH Stage 17 of the Giro d'Italia LIVE, FREE and in HD from 7:50pm (AEST) via SBS On Demand and 8:30pm on SBS VICELAND tomorrow.
