The Nikkei 225 index closed at 13,867.61, up 176.12 points, with export-oriented and high-tech issues benefiting from the weak yen and bargain hunting.
But prices were off their highs ahead of the long weekend and the US unemployment data due on Friday evening.
The dollar was at 116.48 yen, up from 116.26 in late New York trading, and at 0.9564 against the euro, compared with 0.9533 in New York.
Dealers said the dollar was boosted against the yen by Finance Minister Kiichi Miyazawa saying he had no intention of intervening in the foreign exchange market to stem the yen's fall.
Government bond yields were lower, with bond No 225 yielding 1.605% and No 226 yielding 1.615%.
The US 30-year government bond was at 111-26/32, yielding 5.440%, up from 111-21/32, yielding 5.451%, in late New York trade.