Electricity was mostly restored in seven regions, but 15,600 households were still without power as of Tuesday afternoon, according to a local utility.
Part of a pedestrian bridge was swept away in Kyoto and flying debris stopped local commuter trains.
Express bullet trains were suspended as planned along with hundreds of flights, including 240 Japan Airline services and 313 of rival ANA, particularly those serving Osaka.
Around 650 people were forced to stay overnight at Kansai airport, located on an artificial island in Osaka Bay, after rail and road access was cut off by the storm, Kyodo News reported.