Team Jumbo's Vingegaard tops the overall standings 3min 34sec ahead of two-time defending champion Tadej Pogacar, while Geraint Thomas of Ineos Grenadiers, the 2018 winner, stands third at 8min 13sec.
Frenchman David Gaudu of FDJ and Aleksandr Vlasov of Bora round out the top five ahead of Sunday's stage to Paris which is traditionally a ceremonial run. "I'm still proud of myself, I did what I could, and at least I have the white jersey (best under-25s)," Pogacar said at the line.
Saturday's time-trial was won by Wout van Aert ahead of his Danish teammate Vingegaard, meaning Jumbo have six stage wins, the yellow jersey, the green sprint jersey and the polka dot climb jersey.
Van Aert will also be a favourite to win the final day dash around the Champs-Elysees before the jersey winners are crowned on a podium beneath the Arc de Triomphe.