Park needed only six minutes to open the scoring when the Manchester United midfielder surged down the middle before firing home from the edge of the area.
Substitute forward Park Chu-Young added a penalty in second-half stoppage time to seal the win, with both teams hoping to avoid a repeat of four years ago, when they each crashed out in the group stages of the FIFA World Cup.
"My players never lost their nerve in this sell-out stadium and concentrated very well until the end. I think that is the key to the victory," said Korean coach Huh Jung-Moo. "My players played their own play until the end. I'm happy about it. But we must improve further our counter-attacks, we need to do it more sharply."
Huh singled out Park Chu-Young for special praise after the Monaco hitman won the penalty -- felled by home goalkeeper Seigo Narazaki -- that he duly dispatched in the dying minutes. "I was just disappointed that I didn't send Park Chu-Young onto the pitch earlier," Huh added.
The pressure will now be firmly on Japan coach Takeshi Okada after this latest poor showing from his charges, who also lost to Korea Republic at home earlier in the year in the East Asian Championships.
"My players did their best but I feel sorry for the fans that we lost to South Korea twice this year," said a dejected Okada, whose side goes up against Cameroon, the Netherlands and Denmark in Group E in South Africa.
"We needed the result but we couldn't get it and I feel responsible for that," said Okada. "We lost an early goal but I thought we would have some chances. However, we lost a penalty to give an unnecessary goal in the end."
In a game of few chances, Japan's best opportunity in the first-half came in the 20th minute when Vissel Kobe forward Yoshito Okubo shot wide, while CSKA Moscow midfielder Keisuke Honda's shot was saved by keeper Jung Sung-Ryong.
Huh changed his forward line at the interval to Park Chu-Young and Kim Nam-Il, but the visitors rarely looked like adding to their lead as the game threatened to peter out.
As they chased an equaliser, Okada sent on Catania striker Takayuki Morimoto to replace the struggling Shunsuke Nakamura. And Morimoto had a chance to score, but his sizzling shot in the 77th minute was saved.
Korea Republic take on Greece, Argentina and Nigeria in Group B at next month's FIFA World Cup finals.