The 15-year-old beat her 17-year-old compatriot Choi Eun-Kyung by just 0.29 seconds, while Bulgaria's Evgenia Radanova took the bronze.
Pre-race favourite Yang Yang (A), seeking to win China's first ever gold at the Winter Olympics, finished fourth.
The country's number-two Yang Yang (S) careered off with four laps to go when she tried to overtake the leaders.
Choi, who also holds the 3,000m world record, broke the world record in the distance as she clocked 2:21.069 in the semi-finals.
But Choi could not reproduce that form in the final.
"Because it was the Olympics I tried even harder and harder than before. I am very happy for Korea because we won two medals today," said Ko.
Korean woe in men's event
The men's World Cup winning relay team, silver medallists at the last Games in Nagano, were disqualifed from the 5,000m race.
Min Ryoung was judged to have interfered with an Italian skater in the relay semi-final after both tumbled to the ice and crashed into the siding.
Min lay prone for several minutes and eventually was taken out of the rink on a stretcher.