The 36-year-old was the first Asian man to reach a Grand Slam singles final at the 2014 US Open and the second after Thailand's Paradorn Srichaphan to make it into the top 10.
After bowing out at the tournament he won in 2012 and 2014, Nishikori soaked up applause from fans at the Ariake Coliseum as organisers honoured his two-decade career with a video tribute featuring messages from top players including Novak Djokovic.
"We had some great battles at the Grand Slams and other tournaments all over the world," 24-time Grand Slam champion Djokovic said.
"Your resilience and your fighting spirit to always come back after all the adversity you had with your body, injuries, and everything that you faced is really commendable and admirable.
"I'm really glad you're ending your career in your town, in your country, in front of your people. You're definitely going to get the farewell and applause that you absolutely deserve. All the very best in retirement, Kei."
Seven-time Grand Slam champion Carlos Alcaraz said he considered himself a fan, while others like Grigor Dimitrov, Alex de Minaur and Andy Murray heaped praise on his two-handed backhand.
The Shimane-born Nishikori reached his career-high ranking of four in 2015 and claimed 12 titles on the ATP Tour, but has been hampered by injuries for years and has slipped to 436 in the world.
Former world number three and twice Grand Slam runner-up Stefanos Tsitsipas of Greece led the tributes on social media, thanking Nishikori for his hard work and aggressive, counter-punching playing style in a memorable professional career.
"Beyond your remarkable achievements, you captivated audiences everywhere with your one-of-a-kind playing style, bringing immense pride and emotion to people across Japan," Tsitsipas wrote in Japanese on X.
"I've always loved watching your matches, and it saddens me that I won't get to see you on tour anymore. I'll keep cheering you on in whatever you do next."