Yuki Otsu's first-half goal was enough to see off the World and European champions, who had Inigo Martinez sent off five minutes before half-time.
Keigo Higashi, Kensuke Nagai and Hiroshi Kiyotake all went close to adding a second for Japan - with goalkeeper David De Gea forced to produce a string of fine saves.
Brazil, meanwhile, were inspired by Oscar as they had to fend off a brave fightback from Egypt to win 3-2 at the Millennium Stadium.
The midfielder set up Rafael and Leandro Damiao for the first two Brazil goals, before Neymar made it 3-0 at half-time.
Egypt responded after the break and were given hope when Mohamed Aboutrika and Mohamed Salah pulled goals back, but it was not enough.
In Group A, Uruguay came from behind to beat United Arab Emirates 2-1.
UAE captain Ismaeil Matar had opened the scoring midway through the first half but Uruguay responded and after Luis Suarez had been fouled 20 yards out, Bologna midfielder Gaston Ramirez curled them level.
Suarez was also involved in Uruguay's second goal, as he cut inside after collecting a pass from substitute Nicolas Lodeiro, who kept going and struck a clinical shot into the far corner.
Great Britain also looked to be on course for victory at Old Trafford when Craig Bellamy put them in front with a clinical volley early in the contest against Senegal. But Stuart Pearce's men were then pushed onto the back foot and ultimately conceded an equaliser to draw 1-1, as Moussa Konate struck eight minutes from time.
The Host Nation pushed forward in search of a winner and they were unlucky when Marvin Sordell's effort hit the crossbar.
At St James' Park, substitute Raul Jimenez was denied an injury-time winner by the woodwork as Mexico and Korea played out a 0-0 draw.
The striker clipped the outside of the post after being put through by Giovani dos Santos.
Korea enjoyed the better of the first half, with Nam Taehee firing high and wide with 19 minutes gone and Park Jongwoo striking a long-distance half-volley over, while Marco Fabian passed up a glorious opportunity to fire Mexico ahead when he hit his 69th-minute effort over the crossbar.
Earlier, in the opening game of the men's competition, Jerry Bengtson scored twice for Honduras, but they were held to a 2-2 draw by a Morocco team that was reduced to 10 men when Zakarya Bergdich was sent off, while Belarus marked their first appearance at a major tournament since gaining independence with a 1-0 victory over New Zealand.
Belarus midfielder Dmitry Baga grabbed the only goal on the stroke of half-time following a lapse by Michael O'Keeffe.
In Group B, Pierre Aubameyang denied 10-man Switzerland an opening victory as Gabon claimed a hard-fought point from a 1-1 draw.
The St Etienne striker cancelled out Admir Mehmedi's twice-taken penalty with a neat finish as the half-time whistle approached.