Australian O’Connor, 29, took off alone 15km from the finish and navigated the mountain mist to win one minute, 45 seconds ahead of Pogacar atop the Col de la Loze.
Vingegaard crossed the line in third place, nine seconds behind the Slovenian.
“It was brutal, I’ve never lived anything so hard. The team did well and we had a good plan, but I couldn’t take any time off Tadej,” said Vingegaard.
Pogacar now holds a four-minute, 26-second lead over the Dane in the general classification with three days to go before the finish in Paris.
Starting the day with a deficit of four minutes and 15 seconds, Vingegaard had attacked a massive 71km out.
“Our tactics fell apart when they attacked so soon,” said Pogacar explaining he simply tracked his rival on instinct.
Pogacar eventually dropped the Dane near the finish line to gain another 11 seconds on the Team Visma rider who won the 2022 and 2023 Tour de France.
O’Connor, from the Jayco-Alula team, said he was relieved to triumph again four years after his success in the Alps at Tignes.
“Putting your hands in the air is an extraordinary thing. It was about time for me being an Aussie rider in an Aussie team,” said a beaming O’Connor, who joined Jayco in January. “I had to go from the bottom of the valley before the last climb. It was the only way to beat them.”
Pogacar said O’Connor had put in a great ride.
“Congrats to Ben. How he rode today, that’s his victory.” (AFP)