With his team two down, second-half substitute Hassan Abdel Fattah scored twice within seven minutes to pull off an improbable draw for Jordan, who are now second in Group 3 with four points. South Korea are top on five points with Turkmenistan and North Korea playing on Monday.
"We gave up goals too easily," said frustrated Korean manager Huh Jung-Moo, who blasted his team for not killing off the game. "We should have scored more. We grew complacent after building the lead and some guys just tired toward the end."
Korea dominated early on with Manchester United midfielder Park Ji-Sung giving them the lead in the 38th minute, converting a headed pass from Lee Chung-Yong deep in the Jordan box.
They went two up shortly after the break when Park Chu-Young converted a penalty after midfielder Cho Won-Hee was hacked down from behind by Hatem Aqel just inside the penalty area. With Korea in control, substitute Kim Do-Heon almost scored a third but his header, set up by Cho from the right, sailed just over the crossbar.
South Korea paid dearly for the near-miss with Abdel Fattah banging home his own rebound from close range in the 72nd minute with goalkeeper Kim Yong-Dae caught out of position.
Seven minutes later Abdel Fattah struck again. Al Matalka's cross from the left found the charging midfielder unmarked in the box and he rolled the ball in with his left foot past the diving Kim.
Jordan manager Nelo Vingada said he was delighted with the draw, but surprised. "As I've said earlier, South Korea are a better team and I didn't expect we'd score two goals against them," Vingada said. "But we wanted to show Korean fans that Jordan are an improving team. We never gave up after going down 2-0 and our efforts paid off."
The two countries play each other again on June 7 in Jordan. Australia play Iraq in Brisbane on Sunday with the remainder of the Asian qualifying games on Monday.