His team-mate and world champion Lee Ho-suk took the silver while Apolo Anton Ohno picked up the bronze to become the most decorated US Winter Olympian with seven medals.
"Before these Games, people (media) predicted I would get three gold medals and I'm very happy to get two, I have one more to go," Lee, who will compete in the 5000 relay, said.
South Korea, who won three of the four men's medals in 2006, are heading for similar domination this time round. The country also picked up two medals in the women's 1500 metres on Saturday with Lee Eun-byul's silver and Park Seung-hi's bronze.
Ohno won his seventh medal in three Games, surpassing speed skater Bonnie Blair's American record, and said that had he not slipped with two-and-a-half laps to go and lost a lot of speed he could have claimed gold.
"Argh, if I wouldn't have done that slip I could have won the race," he said.
"You make one mistake and you go from second place to last place. I was able to re-group in a very tough race."
His big moment was watched in the packed arena by American 14-times Olympic swimming champion Michael Phelps, as well as a number of fans sporting Ohno-esque bandanas and goatees.
"It feels amazing, it's my third Olympic Games. There's no other (short track) athlete here who has done that," said Ohno, referring to the two golds, two silvers and three bronze medals he has won.
After causing both himself and South Korean team mate Sung Si-bak to lose out on medals in the 1500 final with a careless move that sent them both crashing to the ice metres before the line, Lee Ho-suk made up for his error with a silver.
He said he had watched videos of his past races to try to pick himself up after last week's race.
"What happened in the 1500 was that I was not able to race the race I wanted to. After my injury I couldn't get back my to my normal sense of the race," he told a news conference.
"What I tried to do is have a positive frame of mind for the future so I watched some videos of my past performances."
Canadian brothers Charles and Francois Hamelin were fourth and fifth to the disappointment of their screaming fans.
There were five skaters in the final instead of four after Francois Hamelin was advanced after he was sent hurtling into the safety mats face first after being impeded by American J.R. Celski in their semi-final.
Place of birth: Seoul, Korea
Major previous Olympic results: Gold, 2010 Winter Olympics, 1500m
Gold medallist, 2009 World Team Championships, team
Champion, 2009-10 World Cup, 1000m
Champion, 2009-10 World Cup, 1500m
Runner-up, 2008-09 World Cup, 1500m
Third place, 2008-09 World Cup, 1000m
Lee began skating at the age of 12. The 20-year-old grew up admiring American short track skater Apolo Anton Ohno, the man who finished second behind him in the 1500m and third in 1000m finals in Vancouver.
In the 1500m event, the Koreans had been heading for a clean sweep in the race but Lee's team mates Lee Ho-suk and Sung Si-bak collided and let Americans Ohno and J.R. Celski snatch silver and bronze.