Just like Europe, Japan transitioned from a classical period with a powerful emperor to a medieval period with feudal warlords. In Europe, this transition happened during the 'Dark Ages' - a pretty violent era where technological advances like aqueducts, sewers and bathhouses disappear. How 'dark' was the early medieval period in Japan?
And is there a reason why European and Japanese emperors were both replaced by feudal warlords? Are there some deep underlying socio-economic causes? In general, human organizations tend to get bigger (small bands of hunter gatherers > villages > cities > states > globalized world).
To answer succinctly, there really isn't any parallel for the 'Dark Ages' in Europe. There was no period where massive amounts of knowledge, technology, written records, literature and art forms, etc were lost following a 'classical' era.
To go further, it isn't as if a 'dark age' is inevitable in history so it shouldn't be expected as a matter of fact in history anywhere, Europe or otherwise. As a matter of fact, history in general is not a linear predetermined progression.
Another thing, the Japanese emperor was not replaced. The power and authority of the emperor was reduced and undermined in many places, particularly militarily and in taxation, but the station of the emperor was still incredibly important politically and the station still existed.
The feudal warlords during the Sengoku Period certainly did not replace the emperor. The common people and aristocracy still venerated the emperor and there was definitely political capital in aligning yourself publicly with 'the emperor's will' or having the imperial stamp of approval on your activities.