Pohang, who also lost against Ulsan in midweek, looked to have secured a share of the spoils four minutes from time when striker Kim Eun-Chong cancelled out Han Ji-Ho's 44th-minute opener for the visitors.
However, Busan clinched the points in the 93rd minute, centre-back Park Yong-Ho finding the net to ensure the visitors secured the last spot in the championship round in thrilling style.
Pohang's slip-up allowed Ulsan Hyundai to close the gap at the top of the table to one point after they secured a 2-1 away win at Gangwon.
Ulsan took command in the first half, opening up a two-goal lead thanks to a strike from Brazilian midfielder Caique and an own goal from Choi Woo-Jae.
Gangwon did pull a goal back before the interval through forward Choi Jin-Ho, but they could not find the leveller as Ulsan held on to take all three points.
Jeonbuk Motors are also just a single point behind Pohang following their comfortable 2-0 success over Incheon United, midfielder Thiago Potiguar and Belgian attacker Kevin Oris netting to wrap up the win.
Seoul remain fourth following a slender 1-0 victory over Daegu, Kim Hyun-Sung's seventh-minute goal proving enough for maximum points.
Suwon Bluewings were held to goalless draw against Chunnam Dragons, while goal difference denied Seongnam from reaching the championship round after Ui-Jo Hwang's opening-minute effort secured a 1-0 win at Gyeongnam.
Elsewhere Jeju United defeated bottom club Daejeon Citizen 2-1, Pedro Junior scoring in the 92nd minute after Cesar Arias had levelled things up following Seo Dong-Hyeon's opener.
The K-League now splits in two, with the top seven and bottom seven clubs competing for qualification to the AFC Champions League and to stay in the league respectively.
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