Ryoichi Maeda steered in a point-blank header in the 25th minute for the Asian champions, who lost playmaker Shinji Kagawa to a back strain an hour before kick-off.
"It's three points, we'll take it," Japan coach Alberto Zaccheroni told reporters. "It was an important result. We want to qualify for Brazil as quickly as possible."
"I felt a twinge during training," said United's $21-million pre-season signing. "It's not that serious and shouldn't keep me out for long.
"It's a pity because obviously I wanted to play but I didn't want to risk letting the team down."
The Brazilian's young side came agonisingly close to silencing the crowd of 60,000 in Saitama, both times having close-range efforts blocked.
"We practised that move," said Maeda. "Oka's pass was perfect and I just had to get on the end of it. It was down to him. We knew we had to win but we still have to improve."
A diving header from Keisuke Honda, brilliantly tipped against the post by goalkeeper Noor Sabri, almost doubled Japan's lead in the second half.
"We have the quality to cover the holes if we lose one or two players," Japan captain Makoto Hasebe said of Kagawa's late pullout.
"The teamwork was excellent and we got the three points we wanted but we can play better. We know there are some difficult games away waiting for us."
"We played well and created decent opportunities," said the 59-year-old. "We just couldn't take our chances.
"It was an extremely tough game, as we expected. Japan's players were better prepared so I had to pick players to try and neutralise them but they were too good."
