The dollar sell-off was sparked by news the world's largest auto maker, General Motors, had been subpoenaed by the US Securities and Exchange Commission as part of a probe into its accounting practices.
The news helped the yen climb from 2-year lows weaker than 116 per dollar.
The Korean won recovered to around 1,043 a dollar, closer to the previous day's one-week high, from an intraday low of 1,048.
The Taiwan dollar ended the day steady at 33.66 per dollar, but away from this week's one-year trough of 33.80.
"Dollar/yen was hit so hard above 116. That has put the dollar bulls on a bit of a backfoot at this stage," Sean Callow, Westpac Bank's Asian currency strategist said.
The won and Taiwan dollar had been weighed down by persistent selling of their share markets by foreign investors.
Callow said low interest rates in Taiwan also made its currency unattractive.
Foreigners were net buyers of a tiny amount of Korean stocks on Thursday, following selling for 24 consecutive sessions when they dumped a net $3.15 billion in stocks.
They sold a meagre amount of Taiwan's shares on Thursday. Foreigners had turned net buyers in Taiwan on Wednesday and Tuesday, having been net sellers of more than $1.2 billion of stocks in nine preceding sessions.
"Undoubtedly there is massive real-money selling of Asian equities, particularly north Asia," Callum Henderson, Standard Chartered Bank's currency strategist, said.
Henderson said currencies of economies with less exposure to foreign portfolio flows seemed to have fared better.
"There seems to be a major divergence between Asean currencies and North Asia, which you would expect, given the fact that Korea and Taiwan compete directly with Japan across a number of major industrial sectors in third markets," he said.
Elsewhere, the Chinese yuan hit its highest closing level since being revalued in July, closing at 8.0862 per dollar. Non-deliverable forward markets showed the currency being quoted at a higher forward premium.
"There seems to be a little bit of tolerance there for yuan strength. A slight drift higher, although it is definitely not enough to stop the Americans from complaining," Callow said.
The US administration is due to present its report on currency practices of key trade partners to Congress in November.
Markets have been speculating whether the report will label China a currency manipulator, because the yuan has barely moved since being revalued, and whether China will let the yuan appreciate faster ahead of that report.