The Pohang Steelers striker's worst fears were confirmed by a specialist in Frankfurt on Thursday, where he was informed he had no option but to undergo surgery on his right knee.
"The ligaments have snapped so surgery was the only choice," said Pohang media officer Shin Joo-hyun. "We expect that Lee will take four to six months to recover.
"He won't be able to play any part at the World Cup."
Lee initially decided against surgery after suffering the injury in a K-League game on April 5,
The news that he needs immediate surgery is a shattering blow to the 27-year-old, who was left out of the World Cup squad four years ago by former national team coach Guus Hiddink.
South Korea reached the semi-finals of the 2002 World Cup as co-hosts in Lee's absence but the forward has become a permanent fixture since Hiddink's departure.
Lee, who played at the 1998 World Cup as a 19-year-old, scored some crucial goals during the 2006 World Cup qualifiers and is a favourite of national team coach Dick Advocaat.
(Writing by Alastair Himmer in Tokyo)