After conceding a penalty in just the fifth minute and having defensive midfielder Yhonny Ramirez sent off with 20 minutes remaining, Junior claimed victory at Uniautonoma's Estadio Metropolitano Roberto Melendez thanks to Vladimir Hernandez's late strike.
With league leaders Atletico Nacional losing 2-0 away to Atletico Huila on Wednesday, Junior's victory took them to within five points of the summit as the Colombian title race tightened up.
Uniautonoma took an early lead against Junior thanks to Alan Navarro's penalty and took their lead into the half-time interval.
On the hour mark, Edison Toloza equalised for the visitors after good lead-up work from Luis Quinones but Junior's hopes of victory were dealt a blow when Ramirez received his second yellow card 10 minutes later.
Despite going down to 10 men, Junior kept chasing the game and in the 85th minute, Hernandez scored the winner, sliding in at the back post to poke Juan Guillermo Dominguez's attempted shot into the net.
Junior rose to fifth with the win on 21 points, just behind fourth-placed Santa Fe, who lost 1-0 at Envigado.
Also on Wednesday, Huila struck late in both halves to trump Nacional with Jean Carlos Blanco and Hernan Herchalar scoring the goals.
Nacional (26 points) remain top of the Primera A table with 26 points, two ahead of Millonarios, while Once Caldas, Santa Fe and Junior are all on 21.
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