The benchmark Nikkei 225 index rose 0.13 percent or 27.26 points to 21,319.55, while the broader Topix index was up 0.14 percent or 2.33 points at 1,706.13.
"A rebound in US shares and a relatively weak yen were positive factors today," said Hikaru Sato, senior technical analyst at Daiwa Securities.
"But buying remained limited as investors are still concerned about several uncertain elements, including a US-led trade war," Sato told AFP.
The dollar was trading at 106.56 yen against 106.60 yen in New York on Tuesday, rising from levels below 106 seen a day earlier.
A weak yen is positive for Japanese exporters as it inflates their earnings.
"Japanese stocks are likely to test a rebound as sentiment has improved after sharp rebounds in US shares and the yen's drop to the mid-106 range," Okasan Online Securities said in a commentary.
Masayuki Kubota, chief strategist at Rakuten Securities, said it was "time to buy Japanese stocks for long-term investment" while being on guard against risks in the immediate future.
However on Tuesday Wall Street stocks bounced back from the previous day's rout as tech shares gained.
In Tokyo trade, Honda jumped 1.30 percent to 3,662 yen on the weaker yen and robust US sales results for March.
Toyota gained 0.13 percent to 6,739 yen while Nissan rose 1.00 percent to 1,109 yen.
Market heavyweight Fast Retailing, the operator of Uniqlo clothing chain, surged 2.98 percent to 45,200 yen.
Sony was down 0.25 percent at 5,137 yen after it announced its wholly owned Sony Music Entertainment had sold part of its equity stake in Spotify on its stock debut.
The combined sum of gains from the sale and book value appreciation was about $1 billion based on the sale price and Tuesday's market closing price.
Sony Music had a 5.7-percent equity stake when the music streamline giant soared to a value of more than $26 billion in its long-awaited stock debut in New York.