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Jhonatan Narváez (Ineos Grenadiers) made things very interesting after launching a solo attack with 8 kilometres to go, putting the bunch under pressure to chase as the stage came to a climax in Napoli.
Ultimately it was heartbreak for the Ecuadorian who was swallowed up in the final 500 metres as the sprint trains stormed through, Lidl-Trek on the front with their points leader Jonathan Milan in second wheel.
Kooij smartly stayed in Milan's wheel, and went with the Italian as he launched into the wind, coming over the top to claim an emphatic victory and his first at a Grand Tour.
Tadej Pogacar remained in the maglia rosa having held the jersey from Stage 2 all the way to the first rest day of the race, with the rankings unchanged as Dani Martinez (BORA-Hansgrohe) sits second and Geraint Thomas (INEOS Grenadiers) third.
“This was the step I was looking for, I was really looking forward to my first Grand Tour," Kooij said following the stage after having already won 32 pro races before today. "I think this one is really one I was dreaming of."
“This is what we were looking for, to get a stage win, the first two didn’t go perfect and today we had to fight for it because it was a really tough final. Today we had to just not really stick too much to one plan but just see how the race went, how it evolved and do what was necessary to get me in position.”
It was a disappointing end to the stage for the Australian sprinters, as Caleb Ewan (Jayco-Alula) was boxed in and lost the wheels in the final to finish outside the top 10, with Kaden Groves (Alpecin-Deceuninck) just off the pace to come in seventh.
The race now enters it's first rest day, resuming on Tuesday night (AEST) with a 142km parcours culminating in a summit finish in Cusano Mutri.