The Premier League champions, welcomed to a cauldron of noise with 65,000 packed into Seoul World Cup stadium, fell behind to a 23rd-minute goal from Montenegrin striker Dejan Damjanovic.
Wayne Rooney equalised just after the half-hour mark as United began to get a grip on the game but the South Koreans were back infront before the break after Damjanovic netted his second past goalkeeper Tomasz Kuszczak.
Italian striker Federico Macheda brought United level early in the second half before the visitors introduced Berbatov, Michael Owen and Paul Scholes.
The changes paid dividends as United's pace stretched tired Seoul legs and languid Bulgarian striker Berbatov nodded home to seal the win.
Alex Ferguson introduced hometown hero Park Ji-sung with a quarter of an hour left to play, taking the noise in the stadium to new levels. The energetic midfielder brought the crowd to its feet with every touch but was unable to give the fans the goal they craved.
Ferguson paid tribute to FC Seoul's improvement over the past couple of years. A Cristiano Ronaldo-inspired United had cruised to a 4-0 win over the same opposition two years ago.
"I think in general they're a better team now," said Ferguson. "Damjanovic did very very well. Very good performance tonight.
"It was a very good game, very entertaining. It was the best FC Seoul gave so far. Good pace, good tempo, good intensity."
The Scot added that he had held Park on the bench until late in the second half because his fitness was not at its peak but confirmed he was keen to keep the South Korean captain at the club.
"What happens during the tour doesn't affect what happens on Park's contract," said Ferguson. "We're taking appropriate steps to make sure he's with us for the next couple of years."
Park's team mates were stunned by the reception he received, the crowd going wild when his face appeared on giant scoreboards as he sat on the bench waiting to come on.
"They asked me if I'm the King of Korea," Park said.
Manchester United will wrap up their Asia tour with a game in Hangzhou, China on Sunday. They beat Malaysian opposition twice on the first leg of their tour but had to skip a trip to Indonesia after the deadly hotel blasts in Jakarta.
