Oghenekaro Etebo scored four goals to lead his team to the Group B victory, but here are five things to know from the win.
1. Nigeria thrive in adversity
For opponents Japan, there was something troubling about the smiling faces of the Nigeria team as they finally stepped off their plane in Manaus on Thursday morning.
After the whirlwind of chaos that accompanied their travel arrangements -- arriving barely five hours before their opening game -- the squad looked relaxed as they headed for their hotel. It was soon clear why. The disorganisation around them proved what every Nigerian knows: that the country's citizens thrive under the most adverse of adversity.
Japan could have been forgiven for wondering if the real squad had arrived days beforehand and news of their late arrival was just a smokescreen. It would show on the pitch.
2. Sadiq Umar shows his class to let Etebo star
Umar looked so good for the majority of the game that his agent will almost certainly be fielding phone calls despite the player just signing a new contract at Roma.
His first goal came from taking up position with the awareness of a veteran to poke home from close range, and his hold-up and link-up play free up space to let Etebo to run riot and score his four goals before the 67th minute was over.
Etebo rightly claims the headlines for his goal scoring feat, but Umar was a large part of why he was able to impress.
3. Nigeria's defensive shape needs work
Some things in life are certain: death, taxes and Samson Siasia's team conceding goals.
It's nothing new, and against Japan, one could blame mental fatigue caused by their disastrous travel arrangements. However, going forward, it's hard to picture much by way of defensive improvements.
The team lacked shape in defence, with players running into each other and letting opposition cruise past them as Shinzo Koroki (PEN) and Takumi Minamino struck in the first half, before Asano and Musashi Suzuki caused waves in the final stages.
4. Sincer Seth struggles
Defender Seth made one outstanding play all game: tracking Takuma Asano all the way and making a critical intervention when the newly-acquired Arsenal forward appeared to have broken free.
It was an exemplary piece of defending, but that was ruined completely by being partly, if not fully and directly, responsible for all four Japan goals
5. Mikel John Obi position still uncertain
Usually Mikel plays as a holding midfield for Chelsea and in an offensive position for Nigeria. And, once again, he started at the tip of the midfield for his country.
However, he was so anonymous that the best thing surely be to put him back in his comfort zone. Nigeria might be able to chalk his performance down to travel fatigue and hope he improves before taking any drastic action, but something might need to be done quickly.