It's undeniable that Japan managed to overtake American businesses in key industries, such as silicon and automotive manufacturing, as well as being a world leader in technological innovation.
Japan's small population and land area means that they can never be world leaders in commodity production, such as oil, agriculture, mining, or timber - all of which are industries the USA performs really well in. Oil, specifically, is a crutch relied on by many nations to pad their GDP.
That's why Japan is so incredibly impressive. If you start removing commodities from the GDP comparisons (which are largely based on geographic luck), Japan, is and was an economic powerhouse.
Japan never needed to overtake the economy of the USA in pure GDP, since so much of USA GDP is in areas Japan could never compete in, such as agricultural output, they just needed to overtake the USA in a handful of key industrial areas. Which they did.