Defending champion Geraint Thomas is in second overall with Dutch rider Steven Kruijswijk in third.
Stage 20 on Saturday was won by former winner Vincenzo Nibali who broke from the main contenders late in the final climb.
Bernal and Thomas, co-captains at Team Ineos, crossed the winning line ahead of their key rivals and smiled broadly at each other as they held hands in unity to mark the moment.
Ineos principal Dave Brailsford appears to have masterminded seven tour wins from the last eight editions with Bradley Wiggins, Chris Froome and Thomas having taken six and Bernal within a parade of the latest triumph.
Frenchman Julian Alaphilippe, who led for 14 days before cracking on Friday's weather neutralised stage finished down the field to drop to fifth place overall.
Bernal, who is set to become Colombia's first Tour winner, now leads Welshman Thomas by 1min 11sec and Dutchman Kruijswijk by 1min 30sec ahead of the processionary day of racing ending in the French capital.
Nibali, who won in 2014, came second on this year's Giro d'Italia and while he looked wiped out early in the Tour was radiant when picking up a stage win late in the game.
"To win here is a great joy," said Bahrain Merida's Italian captain.
Saturday's race embarked in cool conditions in 12 Celsius (53.6 Fahrenheit) atop the Val Torrens ski resort at 2,356m altitude.