Japanese shares sold off, with the Nikkei 225 closing down 485.44 points, or 3.05 percent, at 15,434.14, compared with a 1.10 percent decline before the BOJ decision.
The dollar/yen currency pair traded at 103.74 as of 2:41 p.m. HK/SIN, compared with levels as high as 106.02 before the policy announcement. The yen also strengthened against the major crosses, with the euro/yen pair down 1.87 percent at 117.10, the Aussie/yen pair down 2.75 percent at 76.35, while the yen/won pair was up 2.55 percent at 11.29.
The yen's strength came despite mid-day jawboning likely aimed at weakening the currency. Before the BOJ announcement, Japan's chief government spokesman said the yen's moves were being closely watched, calling the appreciation rapid and speculative, according to a Reuters report.
In its policy statement, the BOJ said risks to the economic outlook include uncertainties in emerging and commodity-exporting economies, particularly China, impact of monetary policy response from the U.S. on global financial markets, prospects regarding Europe's debt problem and economic activity, as well as geopolitical risks.
"The BOJ decided a status quo at the June meeting to avoid criticism for a collusive relationship with the government facing the July Upper House election and to save its scarce ammunition before the U.K. referendum next week," said Kohei Iwahara from Natixis Japan Securities, adding further easing could still be in the cards as early as July.
Iwahara added, "The yen is already stronger than most companies feel comfortable at and a dovish Fed could strengthen the yen further, which increases the BOJ's difficulties to achieve its inflation target."
The rest of Asian markets were mostly lower, as investors digested the Federal Reserve's decision to keep interest rates on hold Wednesday.
In South Korea, the Kospi closed down 16.84 points, or 0.86 percent, at 1,951.99.
In Hong Kong, the Hang Seng index fell 1.98 percent in late afternoon trade. Chinese mainland markets closed lower, with the Shanghai composite down 13.73 points, or 0.48 percent, at 2,873.47, and the Shenzhen composite down 4.43 points, or 0.23 percent, at 1,885.43.
That followed gains on Wednesday when the markets largely ignored a snub from MSCI, which made the decision to keep mainland listed shares out of its key emerging markets index.
Bucking the trend, Australia's benchmark ASX 200 gave up gains close essentially flat at 5,145.98.
The Federal Open Market Committee held its interest rate target at 0.25-0.50 percent on Wednesday, after a two-day policy meeting.
In its post-meeting statement, the Fed noted that the unemployment rate had declined (to 4.7 percent), but "job gains have diminished." Fed Chair Janet Yellen said in a press conference following the statement release that the Brexit vote, due on June 23, was also one of the factors in Wednesday's decision.
The Fed's dot plot of future rate projections indicated there was still a greater likelihood of two moves before the end of 2016, but doubts have increased that that will happen.
"The level of confidence in that central case view is now less, with six members anticipating only one hike this year," said ANZ's Brian Martin.
Martin added that while all Fed meetings were considered "live," the market pricing for a possible hike in July had fallen to almost zero. "[The Fed] will need a robust labor market report for June and strong data on retail sales and improving inflation if rates are to move up next month," he said.
Analysts noted that the markets didn't seem to appreciate the dovish bent.
Angus Nicholson, a market analyst at spreadbettor IG, said on Thursday, "Equity markets did not take the release especially well, with U.S. markets closing down for the fifth day in a row...In the wake of the release, gold saw some minor gains, as did emerging market currencies and high yield debt."