With the score tied at 1-1 after goals from Hwang In-Beom and Bahrain's Abdullah Al-Hashsash, Lee turned on the style with two lethal strikes that had the South Korean fans at the small 15,000 capacity arena screaming in delight.
A stop-start encounter had plenty of fouls in the first half and although there was no malice in the challenges, South Korea had three players on yellow cards in the first half hour - including centre back Kim Min-Jae.
The Korean fans had seen enough to start booing the referee whenever he kept his cards in his pocket for a foul from Bahrain and the pressure paid off when Ali Madan went into the book for a tough challenge.
Madan was clearly pumped up and the winger nearly broke the deadlock moments later when he was put through on goal, but his shot directed at the top corner narrowly missed the target.
But South Korea then took the lead through a quick flowing move down the left wing where the ball was crossed into the box and Hwang curled home through a crowd of Bahrain defenders, two of whom ran into each other while tracking back.
Bahrain came out fighting in the second half and they were duly rewarded six minutes in when Al-Hashsash found space in the box and slotted home into the bottom corner.
However, South Korea were not deterred and the east Asian side restored their lead five minutes later through Lee, who pulled the trigger from outside the box and saw his superb effort curl into the net.
The PSG playmaker doubled his tally soon after when he received the ball inside the box from Hwang, escaped his marker with some quick feet and showcased some panache as he curled another shot past the keeper inside the far post.
His second took him joint-top of the tournament's scoring charts alongside Qatar's Akram Afif and Japan's Takumi Minamino.
South Korean skipper Son Heung-min had a late opportunity to score when he was released into the box but his shot went wide while the Tottenham Hotspur forward was also booked for simulation later when he attempted to win a penalty.
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