Vincenzo Nibali collected the stage victory in the Alpine ski resort but the biggest celebrations will be at the Team Ineos hotel, with their 22-year-old Colombian poised to become the youngest winner of the Tour in the post-war era.
Bernal can now enjoy Sunday's traditional procession into Paris, where he will seal a seventh Tour win out of the last eight for his British-registered team, and become the first Colombian to win the Tour.
Last year's winner Geraint Thomas gave his young team-mate a high-five as they crossed the line in Val Thorens, having himself moved up in the general classification to make it a one-two for Team Ineos.
Jumbo-Visma's Steven Kruijswijk will take the bottom step on the podium after Julian Alaphilippe, who started the day second overall after his remarkable run in yellow, cracked once more on the final day.
Bernal, the first Colombian to win the Tour, was almost named the winner without a pedal being turned on Saturday as the bad weather which struck on Friday continued in the Alps, and threatened to see the stage from Albertville, already cut from 130km to 59km, abandoned all together.
But the rain, hail and lightning held off long enough for the race to be run at an aggressive pace given the short distance.
Bahrain-Merida's Nibali, the 2014 Tour winner but never a contender this year after his efforts in the Giro d'Italia, took the stage win out of the breakaway while Jumbo-Visma set the pace behind, looking to shake off Alaphilippe to get Kruijswijk on the podium.
Nibali made the decisive move on the 33.4km climb to Val Thorens 13 kilometres from the summit, just as Alaphilippe was going the other way off the back of the main group.
This was arguably the weakest Team Ineos have looked in their long-running dominance of the race, and yet they emerged with their best result since Sir Bradley Wiggins and Chris Froome occupied the top two steps of the podium in 2012.
They did not take the yellow jersey until Bernal's attack on the Col de l'Iseran paid dividends on a weather-shortened stage 19, and the sight of their riders massed on the front of the peloton setting a pace designed to burn off their rivals has been rare.
But that will not matter to team principal Sir Dave Brailsford, whose investment in the precocious Bernal has paid off even sooner than expected.
Bernal had been pencilled into lead the team at the Giro in May, but after a training crash ruled him out, he turned attention to the Tour, where he expected to be supporting Thomas and Froome.
But after Froome's crash at the Criterium du Dauphine and Thomas' spill at the Tour de Suisse, Bernal was elevated to co-leader status and has repaid the faith shown in him.
Though he did not win a stage – with no victor named on stage 19 where he crested the Iseran first – Bernal was consistently attacking in the mountains to make up for the time he lost to Thomas in the stage 13 time trial.