A Christophe Berra own goal and a side-footed effort by Keisuke Honda in the final eight minutes earned Japan a 2-0 win over a makeshift Scotland at Nissan Stadium in Yokohama.
Berra blotted an otherwise solid performance in the centre of Scotland's defence by scoring an own goal after 82 minutes to give Japan the lead.
And with just seconds remaining, Honda doubled his side's advantage when the Scotland defence failed to clear a cross by Yuichi Komano before the VVV Venlo midfielder stroked the ball beyond Craig Gordon.
Scotland boss George Burley handed debuts to four players for a game that had been blighted in the build-up by the withdrawal of 10 players from the squad in the days leading up to the journey to Japan.
Hearts defender Lee Wallace and a midfield trio of West Brom's Graham Dorrans, Preston's Ross Wallace and Dundee United's Craig Conway were included in the starting line-up, with Stephen McManus wearing the captain's armband.
Atsuto Uchida found space behind Wallace in the 17th minute after being played in by Honda but Kengo Nakamura scuffed his shot harmlessly off target.
With 10 minutes remaining in the first half, the Scotland defence was caught out again by Japan's passing and movement. Naohiro Ishikawa slotted the ball through to Honda, whose pass sent Kengo Nakamura scampering down the left before the Kawasaki Frontale midfielder fired off a shot that could only hit the side-netting.
Burley made two changes at the start of the second half, taking off Wallace and replacing him with Don Cowie while Lee Miller made way for Burnley striker Steven Fletcher.
Within a minute of coming on, Komano played a key role in Japan's opening goal, sending in a low cross that Berra put into his own net, sticking out a leg in an attempt to stop the ball reaching Takayuki Morimoto.
And with barely seconds remaining, Japan doubled their lead after the ball fell to Honda in the penalty area and the Holland-based midfielder side-footed home with glee.
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