Japan lost 2-1 to their Asian Group B rivals at Saitama on Thursday but were denied a 77th-minute equaliser when a close-range shot from substitute Takuma Asano was controversially ruled out by Qatari referee Abdulrahman Al-Jassim.
Television replays were unequivocal, showing the ball floating behind the goal-line in mid air before keeper Khalid Eisa could lay a glove on it and parry it back into play.
"I had a good look at it and I know it went in," Honda, who set up Asano's shot with a downward header and scored the opening goal, told local media.
"It wasn't given so there's no point in going on about it now, but in order to make sure this kind of thing doesn't happen often and there's no doubt, the fourth official has to be there.
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"I was looking for the fourth official but all I could see were the linesmen.
"Of course, I'm not trying to say that the result hinged only on that one incident.
"But when you're playing against improved teams in the final round of the Asian qualifiers and every game is difficult, I would like to see things done at a certain level."
The Japan Football Association had filed a protest over the disallowed goal, Kyodo news agency said, but captain Hasebe said his team should have won without needing to launch an appeal.
"We had enough chances to win the game and spurned them and that is down to us," said the defensive midfielder, whose 100th national appearance was soured by the result.
"Obviously, Asano's shot was a goal but there is not much point in talking about the referee. We took the lead but signed our own death warrant. We were naive in the way we battled and tried to carry the game."
Ahmed Khalil scored twice for the visitors, who inflicted another painful defeat over the team they knocked out of the Asian Cup quarter-finals in Australia last year.
Asian champions Australia, who defeated Iraq 2-0 at home, lead Group B on goal difference ahead of the UAE and Saudi Arabia, who edged Thailand 1-0, after the opening round of qualifiers.
The top two teams will qualify automatically for Russia in 2018, with the third-placed side going into a playoff.
(Reporting by Ian Ransom in Melbourne; Editing by John O'Brien)
