A pair of VAR-awarded penalties swung the game in Ulsan's favour on either side of halftime after Mehdi Abdi gave Persepolis the lead against the run of play in the 45th minute.
Junior's initial spot kick in first-half added time was saved by Hamed Lak before the Brazilian netted the rebound. He made no mistake with his second effort 10 minutes after the break to give Ulsan their first Asian title since 2012.
Ulsan dictated play for most of the first period without creating much in the way of clear-cut chances.
Junior twice headed over from central positions while Ulsan's Yoon Bit-garam went closest to opening the scoring with a shot that clipped the outside of Lak's left post.
As a result, Persepolis were left to try to catch the South Koreans on the break and, after several lack-lustre attempts, they took the lead in the 45th minute through Abdi.
The youngster, drafted into the team for banned striker Issa Alekasir, forced the Ulsan defence to back pedal before hitting a low shot that flew through Davy Bulthuis' legs and beat keeper Jo Su-huk to his right, going in off the inside of the post.
The Persepolis lead, though, was fleeting as Ulsan were awarded a penalty following the intervention of VAR.
Referee Abdulrahman Al Jassim initially missed Yoon being upended by Ahmad Nourollahi but a review saw a penalty awarded to the 2012 winners. While Junior's initial effort was saved by Lak, the Brazilian coolly converted the rebound.
The Qatari official was back at the pitch-side monitor early in the second half to again award Ulsan a penalty, this time when Mehdi Shiri had unnecessarily raised his hand to meet Lee Chung-yong's swinging cross from the right.
Lak was unable to get a hand on the ball this time as Junior sent him the wrong the way to put Ulsan in front with a firm strike to the keeper's left.
Persepolis threw everyone forward in the dying minutes as they sought to erase memories of their defeat in the decider two years ago, but their efforts were in vain.
The final, played at Doha's Al Janoub Stadium in front of a crowd of socially distanced fans, was the conclusion of a tournament that has been largely played in a bio-secure bubble in Qatar due to the impact of the COVID-19 pandemic.