Pre-Tour favourite Roglic has been the form man this season and after Sunday's second-place leads defending champion Ineos leader Egan Bernal of Colombia by 21 seconds.
Yellow jersey holder Adam Yates and other Tour contenders, including defending champion Egan Bernal and favorite Primoz Roglic, crossed the finish line 6 minutes, 40 seconds later.
Jumbo's Belgian all-rounder Van Aert also won stage five and on Friday outsprinted a small leading group.
Briton Adam Yates held on to the overall leader's yellow jersey despite a dramatic late bid by Frenchman Julian Alaphilippe to snatch it back with a trademark kick to the finish that clawed back a few seconds.
Tour de France 2020: Julian Alaphilippe relinquishes yellow jersey to Adam Yates; Wout Van Aert wins stage four
Mitchelton-Scott's Yates took advantage of Alaphilippe's 20-second sanction for drinking water from a bottle at the 17km mark as Belgium's Wout Van Aert won the fifth stage.
Road Cycling World Championships 2019: Great Britain's Geraint Thomas pulls out of men's team trial, to focus on team road race
Thomas remains in the six-man Great Britain team for Sunday's 285km road race from Leeds to Harrogate
Tour de France 2019: Britain's Simon Yates wins stage 12 as Geraint Thomas, Julian Alaphilippe finish together
Simon Yates is over an hour adrift in the overall standings, but punched the air in joy after outwitting his rivals to add this Tour de France stage to victories in the Vuelta and Giro