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Expected to be a stage for the sprinters, the peloton looked to be closing down the four man group of Thomas, Enzo Paleni (Groupama-FDJ), Andrea Pietrobon (Polti Kometa) and Michael Valgren (EF Education-EasyPost) as the line grew nearer, but a lack of coordination meant they were able to stay away.
Pietrobon launched a long-range attack to try and jump his breakaway companions, but Thomas sprinted over the top of the group as they came back together to win his first Grand Tour stage and Cofidis' first of the season.
Tadej Pogacar (UAE Team Emirates) enjoyed a relaxed day to ride home within the bunch and remain in the maglia rosa.
“It was like a long, long team pursuit,” Thomas said of the finish, largely known for his career on the track rather than the road.
"We did an amazing break. I don’t believe it. It was really hard in the final, every pull was full gas. It’s unbelievable.
"With 10km to go we had 40, 50 seconds still and it was a tailwind, so we knew that we couldn’t play with the bunch, and if we were going at 60 kilometres per hour it wasn’t for the bunch to close."
11 seconds behind the break, the sprinters contested the minor placings, with Stage 4 winner Jonathan Milan (Lidl-Trek) quickest to take fifth ahead of Australian Caleb Ewan (Jayco-Alula) who finished sixth.
The race now moves to another slightly hilly parcours in Stage 6, a 180km route from Torre del Lago Puccini to Rapolano Terme which could see the same situation play out again if the sprint teams aren't able to work together again.
