The 22-year-old, bidding to become the first Colombian to win the Tour, embarked on a weather-shortened 59km stage on Saturday with his lead over the key rivals slightly trimmed after an appeal against the original times cobbled together in a scramble.
Bernal now leads Julian Alaphilippe by 45sec instead of 48, Geraint Thomas is third on 1min 11sec and Steven Kruijswijk also closing on the Colombian by five seconds.
Saturday's race embarked in cool conditions with 12 Celsius (53.6 Fahrenheit) atop the Val Torrens ski resort in the rarefied oxygen at 2 356m altitude.
"It may be shortened but it’s one and half hour of climbing, one and half hour of suffering but at the end, there’s a possible victory in the Tour de France," Bernal said at the stage start.
"I’m just as emotional as yesterday but there are 60 very hard kilometres to cover. I’m super motivated with a great desire to arrive at the climb and to do it well," said Bernal
Bernal, who grew up at 2 600m, has thrived at altitude, putting at least 27 seconds into all his rivals on Thursday, before dropping them again as he took the race lead on Friday.
If he survives Saturday, the Ineos co-captain would then just need to cross the line in the peloton at the end of the parade stage to Paris on Sunday to become the first Colombian to win cycling's greatest prize.
"I love my bike, I love adrenalin and coming to these big exciting competitions," said the man poised to become the youngest winner in the modern era.
On Friday, Bernal was racing hard and fast at the head of stage 19 when a violent hail storm and landslides forced scrambling organisers to halt his progress.
"I was going at great speed when they told me to stop and I said: 'no way, not now, please'," he said.
"But they told me it was okay, I was the new leader, and then I accepted it and pulled over," said the youngest man on the race.
Christian Prudhomme, the Tour president, switched into crisis mode when told Bernal and British Vuelta a Espana champion Simon Yates were racing downhill towards a 50cm-deep pile of hail and shale on the road on Friday.
In a snap decision, the Tour halted the racing and declared the times at the preceding summit the official stage results. Organisers later said there would be no stage winner.
Bernal's attack ended Alaphilippe's Tour-defining run in the overall lead that had France dreaming of a first win since Bernard Hinault in 1985.
The style and manner of Alaphilippe's swashbuckling attacks will live long in the memory.
"I don't think I can win the yellow jersey back now," said Alaphilippe.
"I was beaten by something stronger than me."
Earlier, France's other yellow jersey hope Thibaut Pinot was also ruled out.
Trailing behind the peloton in tears, Pinot pulled out an hour into the race, still suffering from the thigh injury picked up in a crash two days ago.
When he dismounted from his bike he ended a roller-coaster ride which included victory atop the first Pyrenean climb to the summit of La Col du Tourmalet, where his performance put him in the frame for a tilt at the title.
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