Wout Van Aert won in Saint-Emilion on Saturday, clocking a time of 35 minutes and 53 seconds over the 31 kilometres from Libourne and winning by 21 seconds from Kasper Asgreen.
Pogacar, the Slovenian 22-year-old of UAE-Team Emirates, will officially claim the yellow jersey after Sunday's final stage to Paris when the leader is not challenged.
His commanding advantage in yellow was never likely to be put in peril on the roads through Bordeaux wine country, and though Jonas Vingegaard took 25 seconds out of him to strengthen his grip on second, Pogacar leads by five minutes and 20 second ahead of Sunday's parade into Paris.
“I'm super happy with the result,” said Pogacar. “I cannot compare (the two titles). They are really totally different. Last year was something else and this is just different."
Additional reporting from PA