Belgian Merlier pipped local hero Jonathan Milan over the line in Padova after 178 kilometres of riding to claim his second victory in this year's Giro.
The Soudal-Quick Step rider had to hold off Milan in the final few metres despite both him and his Italian rival being boxed in towards the chaotic climax of the race.
"Coming from the back is not that easy but we managed well to find a good position," said Merlier.
"I could feel someone coming on the left... then I saw it was Milan on my left and I jumped. A really good jump was necessary."
Merlier's battles with Milan, who retains the cyclamen jersey prized by sprinters thanks to a 127-point lead over Kaden Groves, have been a feature of this Giro.
Milan had used Merlier's wheel to burst through and claim the 11th stage while Merlier also edged Milan on stage three.
The Giro has one more opportunity for the sprinters, in Sunday's final day procession around Rome, with Merlier eyeing a chance to move level at three stage wins this year with Milan.
"It would be nice to have 3-3 but we will see," added Merlier.
Pogacar is seven minutes and 42 seconds ahead of Daniel Martinez with three stages left as he closes in on overall victory.
UAE rider Pogacar is bidding to become the first man to win both the Giro and the Tour de France since the late Marco Pantini in 1998.
"It was a perfect day, with good legs, I'm very happy with my day," said the Slovenian.
The next two stages take the peloton back to the mountains, with Friday's finishing in Sappada close to the border with Austria before Saturday's punishing double climb of Monte Grappa which is the last opportunity to make a move in the general classification.
Pogacar's position at the top of the tree is almost certainly sealed but a podium place is still up for grabs as the Top 10 remains hotly contested.
