All flights are scheduled to operate normally on Friday, a spokesperson from Narita airport said. Flag carrier Japan Airlines said some of its flights may be delayed but that it does not expect any cancellations.
Passengers were stranded at metro stations, while around 1,800 people spent the night at the Chiba Prefectural Government building.
A woman in Chiba's Ichikawa city told NHK the rain "happened all of a sudden so it was a complete surprise".
"The power is out so I'm worried whether I can open my business in the next couple of days," she said.
Meanwhile in the Philippines, authorities have again shut schools and government offices are again shut in most of the country's north, citing the threat of floods.
Earlier this week, Japan, the Philippines and China were hit by back-to-back storms – Dolphin, Chan-Hom and Peilou – churning across the region at the same time.
Dolphin brought heavy rain to Japan's Okinawa island, cutting power to tens of thousands of buildings, toppling trees and cancelling flights.
Over the weekend, Chinese authorities evacuated more than a million people from their homes as Dolphin, the strongest typhoon to hit China so far this year, made landfall in the country's east.