The 7.1 magnitude aftershock on Thursday killed four and cut power to millions of households in parts of the country struggling to recover from the March 11 tragedy while also sparking a tsunami alert, which was soon cancelled.
However, authorities reported no damage to the nation's nuclear power stations.
Tokyo Electric Power (TEPCO) said there were no signs of abnormality at its stricken Fukushima Daiichi plant, which workers are battling to stabilise after it was rocked by last month's twin disaster.
Tokyo's Nikkei surged 1.85 percent, or 177.15 points, to 9,786.08, with stocks again boosted by ongoing weakness in the yen.
Hong Kong put on 0.68 percent in the afternoon and Shanghai rose 0.33 percent.
Seoul ended 0.27 percent, or 5.83 points, higher at 2,127.97.
However, investors remain cautious amid fears that further big aftershocks from the March 11 quake could hurt Japan's production, said Yutaka Miura, senior technical analyst at Mizuho Securities.
Dealers were relieved as it became apparent that Thursday's quake had caused limited damage.
TEPCO jumped 23.52 percent to end at 420 yen.
Market-watchers said Friday's rise in TEPCO came as the Tokyo Stock Exchange imposed a temporarily higher margin rate requirement on new investors, meaning they will have to stump up more cash if they speculate on TEPCO.
Sydney ended 0.66 percent, or 32.5 points, higher at 4,940.6 and Singapore added 0.49 percent, or 15.66 points, to 3,187.31.
Earlier in the day Australian Treasurer Wayne Swan rejected a proposed US$8.7 billion merger between the exchanges saying it went against his country's national interests.
He warned that the deal was more a takeover of the ASX by the Singapore bourse that would see the Australian financial sector become "a subsidiary to a competitor in Asia".
On currency markets the euro edged higher after the European Central Bank on Thursday did as expected and raised interest rates for the first time since July 2008, by 25 basis points to 1.25 percent.
The euro was at $1.4401 from $1.4306 late Thursday in New York, its highest level since January 2010, while the single European currency was at 122.77 to the euro from 122.02.
Against the dollar the yen was at 85.22 from 85.00 yen.
The Australian dollar again climbed versus the greenback after hitting a fresh record high above $1.0500 in late Thursday trading. It fetched $1.0529 late Friday.
The euro was provided support by expectations of another rise later this year, said Kuniyuki Hirai, manager at foreign exchange division at Bank of Tokyo-Mitsubishi UFJ.
"Although ECB president Trichet didn't clarify that Thursday's 25-basis-point hike signalled the start for a string of rate hikes, this does not mean there will be no further rate hikes," Hirai said.
The ECB hike came despite fresh concerns over the region's sovereign debt after Portugal said it would need a bailout to balance its stricken economy, following Ireland and Greece.
Oil stayed at two-and-a-half-year highs because of the ongoing troubles in the Arab world and conflict in Libya as well as the postponement of elections in Nigeria, Africa's biggest crude producer.
New York's benchmark West Texas Intermediate light sweet crude for May delivery rose 93 cents to $111.23 per barrel and Brent North Sea crude for May gained 79 cents to $123.46.
Gold closed at a record high $1,468.50-$1,469.00 an ounce in Hong Kong, well up from from Thursday's close of $1,459.00-$1,460.00.
In other markets:
Taipei ended flat, falling 7.18 points to 8,894.54.
The loss brings to an end a six-day rally for the index.
HTC fell 3.33 percent to Tw$1,160.0 while Acer rose 2.11 percent to Tw$58.1.
Manila closed 0.51 percent or 21.57 points higher at 4,241.00.
Alliance Global rose 0.9 percent to 11.30 pesos and Aboitiz Power was up 1.3 percent at 32.10 pesos but Philippine Long Distance Telephone fell 0.2 Percent to 2,346 pesos.
Wellington fell 0.15 percent, or 5.08 points, to 3,445.28.
Telecom shed 1.0 percent to NZ$1.99, Fletcher Building added 0.2 percent to NZ$9.37 and Ryman Healthcare rose 2.5 percent to NZ$2.48.
Jakarta rose 0.30 percent or 11.23 points, to 3,741.81.
Tin producer Timah jumped 4.6 percent to 2,825 rupiah and consumer goods Producer Mayora rose 4.9 percent to 11,400 rupiah.
Kuala Lumpur ended 0.28 percent, or 4.44 points, down at 1,557.49.
Malaysian Airlines slid 1.6 percent to 1.87 ringgit while construction firm Gamuda dropped 1.5 percent at 3.86 and Hong Leong Bank climbed 2.3 percent to 10.64.
Bangkok edged down 0.60 percent, or 6.52 points, to 1,082.69.
Banpu lost 2.00 baht to 782.00, while Siam cement fell 3.00 baht to 351.00.
Mumbai fell 0.71 percent on Friday, its fourth straight day of losses, as investors’ unwound positions ahead of the weekend, after a recent rally.
The benchmark 30-share Sensex Index closed down 139.73 points to 19,451.45.