Our young midfielder scored the second of England's five penalties only for Martin Hunter's men to lose 5-4 as the shoot-out went into sudden death.
England actually had a chance to win it but Leon Knight's spot kick was saved at 4-4. Japan scored their next penalty and when Craig Pead was also denied, it was all over.
Jacko featured again - his fourth appearance in England's five games - as the game ended 0-0. That meant England went through the tournament without conceding a goal but, on this occasion, neither side looked like breaking the deadlock.
Coach Hunter conceded his players were below par in what was their fifth match in 12 days.
"It was more mental fatigue than physical fatigue and our passing started off well but trailed off,'' he said. "I don't think Japan have played as well against us as in some of their other games, but I don't think we allowed them to do that.
"They had a couple of good strikes at goal which Rhys Evans saved well, but otherwise we had them under control.
"I am disappointed to lose on penalties obviously but we had several good chances and the most disappointing aspect of tonight and the fortnight has been that we didn't convert them."
In the final that followed the England match, Brazil beat Italy 2-0 to win the title.
John Jackson held his nerve - but England lost the third/fourth play-off against Japan in the Toulon Tournament in a penalty shoot-out on Friday.