The midfielder had held up a sign referring to a territorial dispute between South Korea and Japan while celebrating a 2-0 win over their fierce rivals in the bronze medal game in London in August.
"He should receive his medal without fanfare or publicity of any kind," IOC spokesman Mark Adams told reporters after an executive board meeting ruled that the player should be awarded the bronze medal.
The IOC also issued a warning to the footballer and the Korean Olympic Committee over the incident and said the KOC must draw up a programme to educate athletes to ensure there are no repeat incidents in the future.
Asked why the footballer would receive his medal despite the IOC's clear ban on political protests at the Games, Adams said his action in London had not been premeditated.
"It was decided that this was spontaneous and not pre-planned. He also showed sportsmanlike behaviour to Japanese players after the match," Adams said.
Park was handed a sign, which read "Dokdo is our territory", by a fan and was then forced to skip the medal ceremony.
He was also banned by FIFA for two games and fined 3,500 Swiss francs ($3,800) in December.