The Nikkei ended 0.6 percent higher at 21,159.08. Retail and food stocks gained ground, although tech shares came under pressure as they tracked a weakness in their Wall Street counterparts.
All three major US indexes ended lower after a rocky session on Wednesday as gains in consumer staples and healthcare were offset by a sharp drop in Amazon shares and a continuing slide in technology stocks.
Seven & i Holdings gained 1.5 percent, Lawson advanced 1.4 percent and alcohol beverage maker Asahi Group Holdings rose 3.5 percent.
However, Takeda fell 7.5 percent after it said it was at a "preliminary and exploratory stage" of considering a bid for Shire, adding it had not approached Shire's board.
Shire, which sells treatments for rare diseases and attention deficit disorder, said it noted Takeda's statement, and confirmed it had not received an approach.
"Investors are worried that the deal would cause a big debt burden on Takeda, whose market capitalisation is smaller than Shire," said a market strategist in Tokyo.
"It's a bold endeavour it's like a snake trying to swallow its bigger rival and that image is scaring investors. That's not common in Japan."
Tech shares were pressured, with semiconductor equipment makers Tokyo Electron falling 1.9 percent and Advantest Corp shedding 1.0 percent.
The broader Topix advanced 0.3 percent to 1,704.00.