Son was introduced at half-time after South Korea struggled to create attacking opportunities, but the Los Angeles FC star was unable to change the outcome as Bafana Bafana secured a crucial victory.
Hong explained that his decision was based on using Son's pace and creativity against a South Africa side he expected to lose energy after the break.
"We thought that when the opponents had a lot of energy it would be better to use Son later in the game, when they started losing energy and there was more space," Hong said. "We wanted to use him when they were weaker."
However, South Korea were unable to build momentum and Hong admitted his players made too many mistakes, especially in midfield.
"We prepared well, but compared to our previous matches we made too many mistakes in midfield. That's why my players lost confidence," he said.
"We knew how we should have played, but we should have done better. Today's performance was simply not good enough."
The result moved South Africa into second place in Group A behind Mexico and kept their World Cup campaign on track. Bafana Bafana will now face co-hosts Canada in Los Angeles on Sunday as they look to continue their impressive run in the tournament.
South Korea finished third in Group A with three points from three matches, meaning their hopes of progressing now depend on results from other groups.