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Defender Yuki Saneto scored the only goal of the game in the 73rd minute to give Japan their seventh win in seven matches at the Guangzhou Asiad.
In a tight opening half, the UAE shook off the defensive cloak which had frustrated South Korea in the semi-final before delivering a winning sucker punch in extra-time.
They had four shots on target in the first half on Thursday with Omar Al Omoudi having his team’s best chance of the opening period, but he headed wide after earlier seeing a spectacular overhead kick saved by Japan goalkeeper Shunsuke Ando.
Japan had reached the final with an impressive run of six successive wins and boasted the blossoming striking talent of Kensuke Nagai, the 25-year-old having hit five goals in five games.
But it was the UAE who continued to press after the interval with Ahmed Al Abry, who scored the last-minute extra-time winner to beat South Korea, seeing Ando save a close-range header.
Abdulla Bloushi then forced Ando into a smart save at the foot of his post.
The UAE paid for the price for their wastefulness when Japan broke the deadlock in the 73rd minute.
From a flowing move down the left hand side, a cross was swung in which floated over the heads of the UAE defenders and into the path of right-back Saneto.
He took just one touch and fired a right-foot drive into the corner, past the despairing dive of goalkeeper and UAE captain Ali Housani.
Substitute Saeed Al Kathiri then saw a diving header saved by Ando as Japan held on for gold.
Earlier, South Korea stunned Iran with three goals in the last 12 minutes to win the bronze medal match 4-3.
The Koreans looked down and out when Iran went 3-1 in front early in the second half but Monaco’s Park Chu-Young gave them a glimmer of hope when he buried the ball in the net to make it 3-2 on 78 minutes.
In a dramatic finale, Ji Dong-Won made it 3-3 with two minutes of regulation time left before firing in the winner barely a minute later to jubilant scenes on the Korean bench.
