Japan coach Vahid Halilhodzic lamented his players' inability to wrap up their "fantastic" World Cup qualifying campaign with a flourish after a 1-0 defeat away to Saudi Arabia on Tuesday night.

But the Bosnian tactician was quick to defend his team selection in what was an ultimately meaningless match for the Blue Samurai, given they had already booked their tickets to Russia 2018 with last week's 2-0 home win over Australia.

"We have had a fantastic journey on the road to the finals and it is just shame we could not end it with a win," Halilhodzic told the post-match press conference.

Japan had a hatful of chances but came undone when substitute Fahad Al Muwallad struck the clincher midway through the second half to ensure the Saudis would be joining Japan in the finals.

"I looked at the data after the match and we had eight scoring chances and when you have that many you have to be scoring goals," said Halilhodzic.

"We had fatigue and the long travel, heat and humidity played a part but it is true that weren't explosive enough."

"We came very close to getting a victory and the way we played was not deserving of defeat. There were young players in the team that were not used to this kind of match and so we were left wanting when it came to trying to control the ball. We were not gutsy enough but there were positives," he continued.

Halilhozic made four changes to the team that started against Australia, picking veteran midfielder Keisuke Honda despite knowing he lacked match fitness having not played a great deal since arriving at Mexican club Pachuca.

Leicester City striker Shinji Okazaki was preferred up front to Yuya Osako, while Kenyu Sugimoto came off the bench in the second half to make his debut.

"I knew he was not in top condition, that he lacked match fitness as he has not been playing that much for Pachuca," Halilhodizic said of Honda.

"It was my plan just to give him 45 minutes and hopefully he can put in the effort and get his match fitness back."

"Osako was not in the squad because I wanted to put fresh players in and give Okazaki and Sugimoto a chance."

Japan were by far the better side in the first half and Okazaki, Hotaru Yamaguchi and Gen Shoji all went close to opening the scoring in front of over 62,000 fans at King Abdullah Sports City Stadium.

But the complexion of the game changed when Al Muwallad lashed home on 62 minutes, and he could have easily have scored again, such was the threat he posed.

"I expected (Al Muwallad) to come on in the second half and I had already told the players that he would come hard at us," said Halilhodzic.

"They (Saudi Arabia) won the game so I guess it shows that he got his tactics right," he said of the team's Dutch coach Bert van Marwijk.