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.
Pogacar is seven minutes and 42 seconds ahead of Daniel Martinez with three stages left as he closes in on overall victory in the Italian Grand Tour.
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.