The scores remained level on 1-1 after 120 minutes were played at Stadium Australia, and the teams were forced to decide the match by a penalty shootout.
Ali Mabkhout opened the scoring for UAE in the 7th minute by placing his fourth goal of the tournament past Japan keeper Eiji Kawashima and into the bottom right corner. Their early goal gave them confidence while Japan appeared lacking the creative flair that made them tournament favourites.
Japan had few chances in the first half, with Takashi Inui's headed attempt at around the 20 minute mark their best chance of the first half. There were also attempts from Yasuhito Endo and Honda, but UAE keeper Majed Naser was seldom bothered by the Samurai Blue.
Just four minutes into the second half, UAE midfielder Omar Abdulrahman almost helped UAE double their lead with a sublime cross, but Mabkhout couldn't get on the end of it.
Japan looked far more dangerous in the second half , and in the 81st minute Japan found the gap they were looking for, as Gaku Shibasaki scored. Super sub Shibasaki made no mistake as he got on the end of a Honda cross and curled it in to level the scores.
Japan stars Keisuke Honda and Shinji Kagawa missed their penalties during the shootout, Ismail Ahmed scored the winning penalty to gift UAE the 5-4 victory and a spot in the last four.
Extra time saw Japan come close to scoring a winner several times, however, heroic defending from UAE denied them again and again.
The result means UAE will meet Australia in Newcastle on 26 January to compete for a spot in the final.