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Evenepoel, 26, covered the 26.1 km course along the shores of Lake Geneva in 32 minutes and 19 seconds — 28 seconds faster than defending champion Pogacar, who crossed the line second. Every other rider in the field finished more than a minute behind the Belgian, with Denmark's Mattias Skjelmose taking third at 1:04.
The win came on Belgium's national holiday, adding extra significance for the world and the Olympic time-trial champion. It trimmed four-time Tour winner Pogacar's overall lead to 4 minutes and 32 seconds.
Tuesday's victory was Evenepoel's second consecutive stage win, following his triumph in Sunday's mountainous stage 15. It marked his fourth stage win at this year's Tour overall and his third specifically in a time trial. He also extended his gap over Mexico's Isaac del Toro, in third overall, to more than two minutes.
The stage was a difficult one for Evenepoel's Red Bull-Bora-Hansgrohe team. Just two days after two-time champion Jonas Vingegaard abandoned the race following a crash while sitting second overall, teammate Florian Lipowitz suffered a heavy fall on one of the course's bends and was forced to withdraw.