The 20-year-old struck just before half-time, slotting the ball home from close range and past goalkeeper Samuel Cunningham.
"It was a tough match but we are happy because we haven't conceded any goals so far. I feel extremely lucky to have scored the winner," said Higashi.
Japan, top scorers in the tournament with 14 goals, will face either Oman or former champions Iran in the last four.
Thailand, coached by former England captain Bryan Robson, created most of the pressure in the quarter-final clash but were unable to find the finishing touch.
"It's unfortunate. We were the better team over the 90 minutes," said former Manchester United player Robson.
"We passed the ball well and got into good positions, but couldn't convert any of our chances."
Ri Chol-Myong had his kick saved by Ali Housani in the UAE goal before Mohamed Al Shehhi tucked away his spot-kick to send the Gulf side into the semi-finals.
Hong Jeong-Ho put Korea Republic in front after just two minutes, but Sherzodbek Karimov pounced on a mistake by left-back Shin Kwang-Hoon in the 71st minute to equalise.
Uzbekistan played the last 30 minutes of the game with ten men after star striker Ivan Nagaev was sent-off for a second bookable offence.
Monaco's Park Chu-Young, with his third goal of the tournament, restored his team's advantage in the second minute of extra-time with a smart twist and drive which goalkeeper Timur Juraev allowed to squeeze beneath his body.
Kim Bo-Kyung added the third in the 101st minute for an attack-minded South Korean team who peppered the target with 22 shots in the game.