The unit rose to 100.14 yen in late afternoon trade, the first time it has breached the psychologically important barrier since July 5, after ECB head Mario Draghi said Thursday the bank would buy unlimited amounts of debt from troubled nations such as Spain and Italy.
The common currency was also stronger against the dollar, at $1.2677 from $1.2629 late Thursday in New York.
Before the announcement, the euro was trading around $1.2602 and 98.85 yen.
It "will enable us to address severe distortions in government bond markets which originate from, in particular, unfounded fears on the part of investors of the reversibility of the euro", Draghi said.
"We will do whatever it takes" to keep the eurozone together, he added.
Both the dollar and yen have been weak on the yen in recent months as traders increasingly viewed the Japanese unit as a safe-haven at a time of turmoil in Europe and a stuttering recovery for the US economy.
The dollar, meanwhile, was at 78.92 yen from 78.85 yen late Thursday.
"The ECB's bond-buying programme attacks the core of the European debt crisis by relieving some of the pressure on struggling European nations," said Chris Tedder, research analyst at Forex.com in Sydney.
But it was not immediately clear if debt-hit nations would take advantage of the ECB offer, which is dependent on them agreeing to a bailout and undertaking fiscal reforms.
Critics led by Germany had warned that buying the debt of troubled eurozone nations would let them avoid painful austerity cuts that are crucial to repairing their fiscal health.
The announcement "exceeded market expectations, which hasn't happened for a long time", said Dariusz Kowalczyk, senior economist and strategist at Credit Agricole in Hong Kong.
"It draws a line, for a while at least, under the issue of peripheral European debt," he told Dow Jones Newswires.
The dollar's gain on the yen was helped by figures on Thursday that showed US weekly jobless claims fell for the first time in a month while a better-than-expected 201,000 private-sector jobs were added to the world's biggest economy in August.
Investors will now shift their focus to US non-farm payrolls data later in the day, with the outcome a likely indicator of whether the Federal Reserve will launch a fresh round of stimulus.