However, with five minutes of stoppage time on the clock, midfielder Yamaguchi latched onto a headed clearance on the edge of the Iraqi area and smashed the ball home through a crowd of players to earn Japan the 2-1 win.
The victory gave Japan six points from three games, tied with UAE and a point behind co-leaders Australia and Saudi Arabia, who drew 2-2 in Jeddah on Thursday.
The top two teams in Group A and B qualify automatically for the World Cup in Russia while the third-placed teams meet to decide who goes into a CONCACAF-Asian Zone playoff for a place at the finals.
Halilhodzic said he had an inkling that second half substitute Yamaguchi would be a big factor in the outcome of the game.
"I had a pretty good feeling about Yamaguchi today," Japan's Kyodo News quoted Halilhodzic as saying.
"He doesn't score too many goals so I'm really happy for him. I had told both Yamaguchi and (Makoto) Hasebe that if they scored, I'd buy them a glass of champagne.
"But I think he as well as the rest of the team deserve two glasses each."
The win was an important one for the four times Asian champions but they are by no means off the hook. They travel to Melbourne to play the Socceroos next week.
While defeat would plunge their campaign into a fresh crisis and heap more pressure on Halilhodzic, JFA technical director Akira Nishino said speculation that the Bosnian could be sacked was wide of the mark.
"I haven't thought about it at all," Nishino said. "We need to go through games like this. We can definitely build on this.
"The (next) game won't be entirely about winning three points. The team isn't going to dramatically change in two, three days."
(Writing by Peter Rutherford; Editing by John O'Brien)
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