The 29-year-old had spent last season on loan at Bolton, while he has also played for Perugia, AS Roma, Fiorentina and Parma in Italy.
Nakata confirmed to FIFA's official World Cup website: "I will never go out onto the pitch again as a professional football player.
"I had been determined since half-a-year ago that I would finish my career after the World Cup and retire from the football world where I stayed for some ten years.
"After the match against Brazil on June 22, which was my last game, I felt surely I love football. I was very moved, much more than I had expected.
"Coming into the World Cup, I thought the Japanese team had very good potential. The only disappointment was that we couldn't play to our maximum.
"I tried to lead my team-mates in the past four years. I'm feeling sorry that the World Cup ended like this, but I know now that fans had understood what I've tried to do was right."
Nakata scored 11 goals in 77 appearances for the Blue Samurai, having made his debut back in May 1997 against South Korea.
Out of contract Bolton Wanderers defender Bruno N'Gotty is in talks with Birmingham City.
The former AC Milan centre-half has been linked with Reading and Fulham, but Brum boss Steve Bruce has made the first move by opening talks about a Bosman move to St Andrews.
St Johnstone are to run the rule over highly rated Bolton goalkeeper Chris Howarth, 20, next week with a view to possibly taking him on a season long loan.
Former Bolton striker and boss Owen Coyle said, "Chris has been recommended to me by the same people who put us on the trail of Matt Glennon and if he turns out to be what we are looking for then we'll try to bring him in.
"Bolton rate the boy highly and are keen to put him out on loan to get him games. We'll have a look at him in a couple of closed doors matches next week and take it from there."
Former Bolton and France star Youri Djorkaeff was given time off by New York Red Bulls to attend a family emergency back home - and was spotted on TV at the France-Brazil match!