The mostly flat 166km ride from Novara to Fossano was expected to culminate in a sprint finish, but Pogacar had other plans as he powered away with 2km left to ride, followed by Geraint Thomas, but they were caught before the line.

Soudal Quick-Step's Merlier took the stage just ahead of Jonathan Milan of Lidl-Trek with Eritrea's Biniam Girmay taking third for Intermarche-Wanty.

Pogacar's move took everyone by surprise as he went after Mikkel Frolich Honore, but the chasers had just enough time to reel in the UAE Team Emirates rider and Thomas, giving Merlier his eighth win of 2024.

"It was the hardest victory so far, it was a really hard final," Merlier said.

"We caught them back but in the last kilometre, I never found the slipstream anymore so I was always in the wind and I saw 300 metres and was like 'you need to go'."

Afterwards, Pogacar said that it hadn't been his intention to make a break.

"I did not attack, I followed the wheel," Pogacar said.

"It was a good situation, me Mikkel Honore and Thomas. We tried to keep on going but I never believed we could make it to the finish."

Welsh rider Thomas, second overall, had already lost one second to Pogacar in an intermediate sprint, and when the leader joined Honore's break, Thomas was forced to follow suit, and the top two almost made it to the line.

"It wasn't the plan, we just wanted to stay well out of trouble," Thomas said.

"Then I saw Honore and Pog go and then I was like 'might as well just go' but jeepers man that was solid, he was kicking my head in."

Pogacar, who won Sunday's stage two and the overall lead, is 46 seconds ahead of Thomas of Ineos Grenadiers, with Daniel Martinez (BORA-Hansgrohe) a further second behind in third.

Tuesday's stage four should give the sprinters another chance for glory in a 190km ride from Acqui Terme to Andora.