Fast Retailing and its charismatic President Tadashi Yanai will each give 50 million yen to the 24-year-old tournament runner-up, who lost in straight sets to Croatian giant Marin Cilic.
The casual-clothing firm, which operates the Uniqlo brand, saw a run on shirts worn by Japan's best male tennis star during the tournament at Flushing Meadows, which feature the cheap-chic brand's logo.
The firm wanted to congratulate the athlete and celebrate his achievement, and to reward him for boosting both Uniqlo's brand image and the morale of its workers, a company spokesman said.
"We wanted to celebrate his historic achievement," he said. (Almost Missed US Open: Nishikori)
The bonus "was also meant to show our continued support as he aims to be the world's number one," he said.
The bonus comes on top of a runner-up's purse of $1.45 million.
Fast Retailing has been working to make itself a top global brand to rival Zara and H&M, and has opened flagship stores at prestigious addresses in London, New York and Shanghai, as well as at home in Tokyo.
Nishikori became the first Japanese and the first Asian man to play in a Gland Slam singles final, after defeating world number-one Novak Djokovic, who is also sponsored by Uniqlo.
Nishikori's performance in New York led the news in Japan for days and dominated all sorts of television programmes and newspapers, with the semifinal between Nishikori and Djokovic touted as a showdown between two Uniqlo players.
Even after the youngster came undone in the final, crushed by Cilic 6-3, 6-3, 6-3, his cheerful but humble demeanour further endeared him to Japanese fans.
The final between the two younger stars was also seen as a possible signal of the end of dominance by the Big 4 -- Djokovic, Roger Federer, Rafael Nadal, and Andy Murray.
It also showcased a possible future without established sports brands like Nike or Adidas, with Cilic wearing shirts from China's Li-Ning sport brand.