The Nikkei 225 rose 9.07 percent while the broader Topix index of all first-section shares tacked on 9.93 percent since January -- ahead of most major markets in the US and Asia-Pacific.
The positive finish marked the fourth year of gains for the Japanese market, although the Nikkei is sitting below its June highs.
The index was near the 21,000 level before China's shock currency devaluation this summer hammered equity markets as it aggravated worries about the powerhouse economy -- a major driver of global growth and a key market for Japanese firms.
On Wednesday, the last trading day of the year for the Japanese market, the Nikkei ticked up 0.27 percent, or 51.48 points, to close at 19,033.71.
The Topix rose 0.25 percent, or 3.91 points, to 1,547.30.
Analysts were generally upbeat on the prospects for Japanese equities in 2016, saying the yen would remain weak on expectations of more monetary easing by the Bank of Japan, as it looks to counter sluggish growth in the world's number three economy.
A weak yen boosts the profitability of major exporters such as Toyota and Panasonic and lifts investor demand for their shares.
The past year saw Japan unveil a long-awaited corporate governance code to improve firms' transparency, to try to attract more overseas investors.
The national pension fund -- the world's biggest -- also helped boost the market in 2015 as it ploughed more of its bond-heavy portfolio into domestic and international stocks.