Junior got the scoring going after 29 minutes before Luis Maranhao put them two up after 37 minutes.
Junior notched before the break, before the home side struck back after 57 minutes.
The 26-year-old completed his hat-trick after 76 minutes before Milos Bosancic scored a last-minute penalty consolation.
Kyung Hyun Im scored a late leveller to help Chunnam Dragons to a 1-1 draw with Incheon United, for who Kyo-Won Han gave a 35th minute lead.
Daejeon Citizen and Busan I'Park as well as Daegu versus Gangwon ended goalless.