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It was a spirited performance from the Oceania champions, who defended with great resolve throughout the match but fell behind to a wonder strike from Toshihiro Aoyama in the 66th minute.
The game opened up in the final 20 minutes and in injury time Auckland City even threatened a Cinderella finish, with Adam Dickinson finding himself in space 12 yards out but lifting his shot just over the bar.
"That would have been special," said coach Ramon Tribulietx, "but it wasn't to be. We are all very disappointed but overall we have to be pleased with our performance. It is a massive task to come to Japan and take on the J-League champions. They have fantastic players and obviously are a better team than us."
"It's hard to sum up how we feel," said captain Ivan Vicelich. "It's hard to be positive when you lose but we performed well. For long periods I thought we were dealing with everything that they had to throw at us even though they were creating a lot. We were hanging in there well."
Hiroshima coach Hajime Moriyasu paid tribute to Auckland City, after promising earlier in the week that his side "would show them how the game is played at J-League level".
"That fought very hard and were physically quite strong," said Moriyasu, "so they made it hard for us. But we knew that if we kept playing football they would get tired and I think that is what happened in the last 30 minutes."
For Auckland City goalkeeper Tamati Williams was outstanding, making several fine saves including a double stop moments before the Hiroshima goal. Vicelich and Angel Berlanga comprised a solid defensive wall at the back and Albert Riera was a tireless worker in midfield. Dickinson showed great strength and determination as he often ploughed a lone furrow up front while Luis Corrales added impetus as a second half substitute.
Apart from goalscorer Aoyama, the entire Hiroshima midfield had solid matches, with Mihael Mikic creating havoc down the right hand side as the local team enjoyed almost 60 per cent of possession across the match.
On a bitterly cold night in Yokohama, coach Ramon Tribulietx opted for his traditional 4-3-3 formation, with Andrew Milne replacing the injured James Pritchett at right fullback and Williams getting the nod in goal.
Auckland had precious few chances in the first half and had to wait almost 12 minutes for their first sustained spell in possession. The opportunities that did come weren't capitalised on; twice Dickinson flashed crosses across from near the byline but nobody was present to take advantage.
They also forced the first corner of the match and had free kicks in promising positions but all were wasted by poor execution and delivery.
The boisterous Hiroshima fans among the crowd of 25,174 were on their feet several times in the first half - Williams was forced into a double save moments before the Hiroshima goal and made several other fine stops.
As well as Aoyama's long range strike, which looked to be heading over the bar but dipped wickedly into the net, the Japanese side also shaved a post and hit the crossbar with other attempts.
Sanfreece Hiroshima 1 (Toshihiro Aoyama 66'), Auckland City 0. Halftime: 0-0.
- Michael Burgess of the Herald on Sunday in Yokohama