By Agence France-Presse
The Nikkei 225 index gained 0.37 percent, or 82.74 points, to close at 22,614.82, while the broader Topix index was up 0.15 percent, or 2.46 points, at 1,695.31.
Shares opened lower as the US said it will pull out of a decades-old nuclear treaty with Russia, which Donald Trump accused the country of long violating.
Russian deputy foreign minister Sergei Ryabkov warned withdrawal "would be a very dangerous step".
Adding to the unease were brewing tensions between the US and Saudi Arabia after Riyadh conceded journalist Jamal Khashoggi, a critic of the government, had been killed inside the country's diplomatic compound in Istanbul.
"But bargain-hunting emerged as investors focused on companies expected to report positive results ahead of corporate earnings season," said Daiwa Securities senior technical analyst Hikaru Sato.
"Recoveries in Chinese shares also encouraged Japanese investors to buy back shares," Sato told AFP.
The dollar fetched 112.70 yen in Asian afternoon trade, against 112.50 yen in New York late Friday, with a rise in US Treasury yields offset by risk-off sentiment, dealers said.
"The 112 yen level is still positive for Japanese firms," Sato added.
In Tokyo, Nippon Sharyo plunged 7.30 percent to 2,601 as news reports said the firm was the manufacturer of the express train that derailed and flipped over in Taiwan at the weekend.
China-related shares erased early losses, with industrial robot maker Fanuc rising 0.46 percent to 19,265 yen and electronic parts maker Rohm trading up 0.67 percent at 7,430 yen.