The Brazil striker scored with a firm shot from outside the penalty area, connecting with the ball after Fred controlled a long cross from Marcelo with his chest. The ball bounced only once before Neymar smashed it in.
For the next two minutes, most of the 67,432 fans at the National Stadium chanted Neymar's name, relishing the knowledge that their poster boy is already starting to deliver for the national team with one year to go before the World Cup.
Take that: Neymar opened the scoring with a perfect long-range strike which flew beyond the goalkeeper and nestled in the back of the Japanese net (below)
Party time: Chelsea star David Luiz gets involved with the celebrations
Match facts
Brazil: Julio Cesar, Dani Alves, Thiago Silva, Luiz, Marcelo, Oscar, Gustavo, Paulinho, Fred (Jo 81), Neymar (Lucas Moura 74), Hulk (Hernanes 75).
Subs Not Used: Jefferson, Fernando, Dante, Filipe Luis, Jean, Rever, Bernard, Jadson, Cavalieri.
Goals: Neymar 3, Paulinho 48, Jo 90.
Japan: Kawashima, Konno, Nagatomo, Uchida, Yoshida, Endo (Hosogai 77), Honda (Inui 88), Kiyotake (Maeda 51),Kagawa, Hasebe, Okazaki.
Subs Not Used: Nishikawa, Inoha, Gotuko, Sakai, Havenaar, Nakamura, Kurihara, Takahashi, Hiroki, Sakai, Gonda.
Booked: Hasebe.
Att: 68,000
Ref: Pedro Proenca (Portugal).
Subs Not Used: Jefferson, Fernando, Dante, Filipe Luis, Jean, Rever, Bernard, Jadson, Cavalieri.
Goals: Neymar 3, Paulinho 48, Jo 90.
Japan: Kawashima, Konno, Nagatomo, Uchida, Yoshida, Endo (Hosogai 77), Honda (Inui 88), Kiyotake (Maeda 51),Kagawa, Hasebe, Okazaki.
Subs Not Used: Nishikawa, Inoha, Gotuko, Sakai, Havenaar, Nakamura, Kurihara, Takahashi, Hiroki, Sakai, Gonda.
Booked: Hasebe.
Att: 68,000
Ref: Pedro Proenca (Portugal).
Paulinho added the second goal for Brazil in the 48th minute, deftly controlling a cross from Dani Alves before turning inside and shooting.
Japan goalkeeper Eiji Kawashima got his hands to the ball, but it was too powerful for him to stop.
Former Manchesteer City misfit Jo got the third, latching onto a through ball from the brilliant Oscar and sliding it past Kawashima in injury time.
The win puts Brazil at the top of Group A with three points. Italy and Mexico will play in the other group match on Sunday.
Neymar entered Saturday's match facing a minor wave of criticism. He has become something of an idol in Brazil, but a nine-match scoreless streak had heaped pressure on the 21-year-old striker heading into the Confederations Cup.
The fickle Brazilian fans, who had taken to booing their team in recent weeks, were firmly behind the 'Selecao' and its star this time, however.
Double trouble: Paulinho struck to add to Brazil's lead as they earned a tidy victory in the tournament opener
Hoisted: Paulinho is raised up onto his team-mate's shoulders after bagging the second
All together now: The Samba stars looked a force to reckon with on the opening day
With his hair long on top and short on the sides, Neymar has already started to transcend the game in Brazil, like David Beckham nearly everywhere else. His picture is plastered around the country in underwear and phone ads, to name a few. He has also appeared on Brazilian TV, appearing as himself in one of the country's biggest soap operas. That's just off the field. On it, Neymar has earned himself a massive transfer from local club Santos to Barcelona, where he will be teammates with Lionel Messi next season.
The match against Japan was likely something Neymar was looking forward to. The Japanese have never beaten Brazil in 10 games, earning only two draws - both at the Confederations Cup, first in 2001 and then again in 2005.
The last time they played, in a friendly in Poland in October, Neymar scored two goals. This time, he was named 'Man of the Match'.
Not everything was perfect for the young star on Saturday, however. In the 15th minute, Neymar was stuck on the sidelines fiddling with the socks on his right foot. He came back on the field about two minutes later - after the fans took a moment to boo referee Pedro Proenca for not letting their star back on more quickly.
Midway through the second half, he was briefly knocked down. When he got back up, the fans started chanting his name once again.
And then, about six minutes later, Neymar was taken off and replaced by Lucas. The decision halted the Neymar chants, but not the cheers for Brazil from the yellow-clad faithful.
How about that? Former Manchester City striker Jo tucked the ball away for the third goal late on
Unhappy: Southampton's Maya Yoshida holds the net sadly after Brazil scored their third
Impressive: Oscar put in a superb display and set up Jo's goal to put the cherry on the cake
Turn up for the books: Not many thought Jo would go on to do much after leaving Man City
All lit up: The National Stadium
Shocking scenes: Riot police shoot during a rally to protest against the allocation of funds towards the Confederations Cup and next year's World Cup at a time when Brazil is in dire need of investment in other areas
Riot police arrest a protester during the rally near to the Estadio Nacional Mane Garrincha
Marco Antonio Cumsille, twice National Sport Journalism Awards, covering the Brazil 2013 Confederations Cuo.
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