The dollar was last down 0.4 percent on the day at 99.00 yen, having earlier risen as far as 99.66 yen on Reuters data, its highest since May 2009.
(Read More: Weak Yen Puts Japan Current Account Back in Black)
Traders also cited strong demand to take profit on dollar gains before 99.73 yen, the 50 percent retracement of the dollar's fall from the June 2007 peak of 124.16 yen to a record low of 75.35 set in October 2011.
The euro hit 129.93 yen on Reuters data, its highest since January 2010, before stalling just shy of 130. It last traded up 0.2 percent at 129.50 yen.
Traders cited large stop-loss buy orders at 130 yen.
Japanese Finance Minister Taro Aso said on Tuesday that the yen was undergoing a correction from previous "excessive" rises, though he stressed the country's monetary policy was aimed at beating deflation, not weakening the yen.
Dollar/yen one-month risk reversals, a measure of the relative demand for bets on the dollar rising against the yen over bets on it falling, have risen to around 0.7 in favor of yen puts since the BOJ announcement.
With the dollar stalling ahead of the 100 yen mark, however, risk reversals have dropped back to around 0.5 in favor of yen puts. But analysts said this pause was temporary.
"Dollar/yen has moved so quickly it is bound to have setbacks ahead of key levels, so I am not surprised it is not just flying through the 100 mark," said Niels Christensen, currency strategist at Nordea in Copenhagen.
"(But) ... everything is pointing to a weaker yen and everyone is happy to go with the flow."
(Read More: Yen Headed for Another 10% Drop: Chartist)
Against the dollar, the euro was up 0.6 percent at $1.3083, having hit a more than three-week high of $1.3098 after stop-loss buying was triggered near $1.3050.
Concerns about the euro zone—the bailout for Cyprus, political uncertainty in Italy and Spain's struggling fiscal and economic conditions—seem to have taken a back seat for now, strategists said.
Rating's agency Moody's warned on Tuesday that prospects of Spain missing its public deficit target this year could result in its sovereign credit rating slipping below investment grade.
Higher-yielding commodity currencies, which tend to benefit when equities rise, hit multiyear highs against the yen.
The Australian dollar hit its highest since July 2008 at 103.82 yen and the New Zealand dollar dollar rose to its highest since February 2008 at 84.35 yen.
Against a basket of major currencies, the dollar index fell 0.5 percent to 82.36.
The dollar also fell to a more than five-week low of 0.9304 Swiss franc, before recovering slightly to 0.9326 franc, down 0.2 percent on the day.