South Korean fans hurled debris and officials accused visiting coach Carlos Queiroz of making an obscene gesture Tuesday as Iran beat the hosts 1-0 to reach the World Cup after a bad-tempered qualifier in Ulsan.
Iran scored in the second half and against the run of play to qualify top of Group A and give South Korea some nervous moments, before they also went through on goal difference following Uzbekistan's 5-1 win over Qatar.
As the Iranian players grabbed national flags and celebrated on the pitch at Ulsan Munsu Football Stadium, angry home fans threw plastic water bottles and other items.
And a Korean Football Association official said at the same time, Queiroz made a hand gesture at rival coach Choi Kang-Hee, which incensed some of the Korean players so much that they had to be restrained from running to the Iranian bench.
The scenes brought an unsavoury end to a game already tainted by some unusually harsh trash talk, after South Korea pledged to "make life painful" for Iran and to force their captain to cry "tears of blood".
In return, Queiroz called the comments "shameful" and accused South Korea of taking it easy in their 1-0 loss to Uzbekistan, in a bid to keep his team out of the World Cup.
This week, pictures circulated on Twitter of the former Manchester United assistant boss wearing a picture of Choi taped to his T-shirt, in an apparent joke.
But despite the acrimonious build-up, the game started in tepid fashion.
Ex-Middlesbrough striker Lee Dong-Gook tested Rahman Ahmadi with a stinging attempt from distance and Son Heung-Min fired over in the 21st minute, but any goal would have been disallowed as the referee blew for a foul by Kim Shin-Wook.
South Korea were firmly on top without creating clear chances, and Lee Myung-Joo's penalty shout, when he was clattered on the edge of the box on 40 minutes, was one of their best opportunities of the first half.
Iran started the second period with more ambition and on the hour, they were suddenly in front thanks to a defensive howler from Kim Young-Gwon and the alert thinking of Reza Ghoochannejhad.
Defender Kim failed to make a simple clearance on the right touchline and had his pocket picked by Ghoochannejhad, who scampered goalwards and bent a left-footed shot around Jung Sung-Ryong.
South Korea pressed desperately for the equaliser and Kim Young-Gwon nearly made amends for his mistake when he put a free header wide near the end. Lee Keun-Ho also nearly headed the leveller in injury time.
However the Taeguk Warriors clung on to Group B's second automatic qualifying spot on goal difference, despite Uzbekistan's 5-1 win over Qatar in Tashkent, which finished a few minutes later.
"It was a very difficult match. We knew that we played a great team," Queiroz said. "My team played with a realistic approach, to try and wait for a weak point in the Korean team and with a counter-attacking attitude.
"The goal came in one of those situations and fortunately, when Korea created opportunities, our players fought for our lives. The team played with fantastic team spirit with great practical discipline and enormous determination."
South Korea's Choi, who is now stepping down from the job, preferred not to comment on his row with Queiroz and said he hoped the team could now "start anew".
"I take the full responsibility for this result. Even though we're going to the World Cup, I think we have to start anew," he said. "I hope this defeat will serve as the opportunity for South Korean football to take the next step."