Oman had not lost at home in the final round of qualifiers and Ahmed Mubarak's 77th-minute free-kick looked like preserving their unbeaten streak, after Hiroshi Kiyotake's first goal for Japan had put the visitors in front after 20 minutes.
But Okazaki had the last word when he scored from close range after a break down the left, putting Alberto Zaccheroni's men provisionally eight points clear at the top of Group B with three games to play.
"I'm pleased I was able to score because I didn't do much else for the whole of the match," Okazaki said. "We kept chipping away and found a way to win in the end. We weren't in control today so I hope we can dominate to beat Jordan next time."
Japan were weakened by the injury-enforced absence of Manchester United midfielder Shinji Kagawa and Schalke defender Atsuto Uchida, while Hiroki Sakai started at right-back in place of Yuichi Komano, who hurt his back in training.
Oman looked dangerous on the break and should have taken the lead after ten minutes, but Fawzi Bashir blazed over from a promising position after being picked out from the right wing by Ismail Al Ajmi.
Stuttgart's Okazaki, who missed Japan's recent friendlies against France and Brazil, saw a couple of half-chances saved by Oman's Wigan Athletic goalkeeper Ali Al Habsi at the other end, before Kiyotake broke the deadlock.
Oman failed to properly deal with Yuto Nagatomo's cross from the left and Nurnburg midfielder Kiyotake seized on the loose ball to slot home from close range.
Okazaki winner downs Oman
The goal settled nerves but Oman were unlucky not to be on level terms in the 36th minute, as Al Ajmi headed against the post and Nagatomo hacked the ball to safety, before Al Ajmi was taken off injured.
Kiyotake and Sakai both had chances to extend Japan's lead as the pace slowed, but with 13 minutes remaining, Mubarak squeezed in a low free-kick which sent the home fans into a frenzy.
However, as Oman pressed for the winner, substitute Gotoku Sakai raced free on the left flank and his cross was flicked on at the near post by Yasuhito Endo, leaving the arriving Okazaki with the simplest of finishes. Japan resume their qualifying campaign away to Jordan on 26 March, when Oman are away to Australia.
"We had set ourselves the target of three points here, and I'm happy we accomplished that goal," Japan coach Alberto Zaccheroni said. "The heat meant we couldn't play the way we're capable of playing. Oman showed a lot of heart but I'm proud of the way my team refused to give in."
Oman coach Paul Le Guen commented: "We played against one of the best teams in the world at the moment and we had a great performance so we are very disappointed with the result, the manner in which we lost. There are still three games to play and we are still in the running to qualify."