On Monday footage from Japanese broadcaster TBS showed schoolchildren slipping through snow and ice on their way to class and helping push a teacher's car stuck in the drifts in the northern city of Sendai.
The storm dumped 13.8 inches of snow on the area, parts of which were devastated by the March 2011 tsunami, the heaviest fall recorded there in 78 years.
In nearby Ishinomaki, the drifts surrounded temporary housing erected for people left homeless by the disaster were the most snow they had seen in 91 years.
As much as 10.6 inches of snow fell on Tokyo by late Saturday, the most in 45 years, Japan's Meteorological Agency said.
Snowdrifts and frozen slush choked the roads on Monday morning, forcing commuters in heavy boots to pick their way carefully to work and disrupting public transport.
"We've just got to get on somehow," one schoolgirl said, waiting to squeeze onto one of the few buses in operation in Chiba, outside the Japanese capital.
"But the buses are stopped - I don't know what we're going to do," one of her classmates added.
Traffic accidents and falls claimed 13 lives across the nation - including one 78-year-old man in Ichikawa, just east of Tokyo - and some 1,700 were injured, Japanese broadcaster NHK said.
Flights were still backed up at Tokyo's Haneda international airport on Monday and the lobby was packed with anxious travelers, with some flights overbooked.
"I never thought I'd have to do this at my age," one woman, who appeared to have spent the night at the airport, told TBS.
Some 5,000 people were stuck at Narita international airport at the weekend when the snow cut transport links to downtown Tokyo.
More than 20,000 households were without electricity early on Sunday after the snow and high winds took down power lines.
But financial markets opened normally on Monday as snow thawed in Tokyo, shrugging off the weekend's heavy snowfall.
Thirteen people died and more than a thousand were injured in Japan after the worst snow storm in decades swept the country.