Edison Toloza's 55th-minute goal saw Julio Comesana's men to the hard-fought win at their Estadio Metropolitano Roberto Melendez home.
Junior, seven-time champions, last won a title in 2011 and need another result at Atletico Nacional's Estadio Atanasio Girardot on Wednesday to add to that crown.
The win extended Junior's unbeaten run to six matches, while Atletico's struggles continued.
Perhaps affected by their run to the Copa Libertadores quarter-finals, Atletico have lost four of their past five matches in all competitions.
It was a scrappy winning goal for Junior, with Toloza tapping in from close range after a corner went uncleared by the visitors.
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