The Malaysian champions will be joined in the knockout rounds by Thailand's Buriram United, who confirmed their progress with a 2-2 draw against Gwangju FC.
Shanghai Shenhua, meanwhile, kept their slender hopes alive with a 4-2 victory over Vissel Kobe after the Japanese sent a weakened squad to China, while Kawasaki Frontale eased to a 2-0 win against already-eliminated Central Coast Mariners.
Kawasaki lead the 12-team standings with 18 points from their eight matches, two more than compatriots Yokohama F Marinos, who take on Shanghai Port on Wednesday, with Kobe in third. The top eight finishers advance to the next phase.
JDT moved up to fourth with victory at home over the three-times Asian champions, the Malaysians coming back after going behind to a Lee Ho-Jae header in the 27th minute.
Oscar Arribas levelled 10 minutes later and JDT stepped up a gear in the second half as goals from Bergson and Arif Aiman gave the hosts a two-goal cushion.
Kang Hyeon-Je reduced the deficit with 10 minutes left but, with Pohang pushing for an equaliser that would salvage their qualification hopes, Jese scored on the counter and Jorge Obregon's penalty deep into injury time sealed the win.
"We were very motivated to approach this game because it's the last game before the round of 16," said Bergson. "JDT are stronger than ever and we are more motivated than ever."
BURIRAM UNITED PROGRESS WITH GWANGJU DRAW
Gwangju dropped to fifth following their 2-2 draw with Buriram United, who sit in sixth having squandered a two-goal lead against the South Koreans.
Guilherme Bissoli put the visitors in front in the 13th minute and Martin Boakye added a second 10 minutes before the break but a second-half double from Oh Hu-seong earned Gwangju a share of the points.
Shanghai Shenhua made the most of Kobe's decision to leave most of their key players at home to hand the J-League champions a 4-2 loss that prolonged the Chinese side's qualification hopes.
Saulo Mineiro hit a hat-trick against an inexperienced Kobe line-up that saw goalkeeper Powell Obi sent off in the seventh minute.
The result moves Shenhua up to seventh, level on 10 points with compatriots Shandong Taishan, who face an Ulsan HD team on Wednesday that has already been knocked out.
A draw or win for Shandong coupled with a victory for Shanghai Port against Yokohama F Marinos would see Shanghai Shenhua slip out of the top eight and be eliminated.