Matej Vydra was the first Watford player to fashion a chance, but he could only fire his free kick high over the bar.
On the half-hour mark Rotherham threatened when Craig Morgan headed just over the bar from Pringle's corner.
Paul Taylor was close for Rotherham moments later, but after cutting inside from the left, he curled his effort over the bar.
After a goalless first half, the hosts almost took the lead a minute after the restart, but Taylor fired over after being picked out by Pringle.
With three minutes left to play Munari added a second for the visitors when he finished from close range to seal the three points.