Autumn is one of the most comfortable seasons in Japan. Not too hot or too cold. Here, we have the average temperature in Tokyo in these three years. Please refer this when you are considering what to wear. If you plan to take a trip to Hokkaido or Tohoku areas, they have a little colder temperature than Tokyo, especially in November.
In September, temperatures tend to be around 23ºC to 28ºC (73°F to 82°F) in the afternoon and drop to about 18ºC to 21ºC (64°F to 70°F) in the morning and at night.
In October, afternoon temperatures range from 19ºC to 23ºC (66°F to 73°F), and morning temperatures tend to be around 14ºC to 18ºC (57°F to 64°F).
In November, afternoon temperatures are about 14ºC to 18ºC (57°F to 64°F) while morning and evening temperatures are 7ºC to 12ºC (45°F to 54°F).
Although there is a chance that typhoons may occur between September to mid-October, the weather is comparatively comfortable in autumn.
In September, only T-shirts are enough in the daytime, but you may feel a little cold in early morning and at night. It’s better to wear long-sleeve shirts or put a jacket/coat in October and November. You would need a coat in the late November. Northern Japan including Hokkaido and Tohoku region gets cold earlier than other areas.
In a cold weather, I always have a skin breakout which the face of my skin becomes sensitive, dry and itchy.