Santa Fe and Once Caldas had entered the penultimate weekend of the Clausura regular season level on 28 points but both lost to miss the chance to leapfrog leaders Medellin, who drew 1-1 with bottom club La Equidad on Saturday.
After Santa Fe had lost to Atletico Huila 1-0 earlier on Sunday, Once Caldas travelled to Barranquilla to face Junior but a brace from the home side's Jorge Aguirre saw the visitors continue their winless streak.
Aguirre gave Junior the advantage in the 30th minute after a fine pass from Jarlan Barrera and then the home side weathered a second-half storm thanks to a brilliant performance from goalkeeper Sebastian Viera.
The Uruguayan shot-stopper made a handful of top saves, including thwarting Once Caldas striker Sergio Romero from the spot, before the visitors lost Jaime Sierra to a second yellow card with five minutes remaining.
With a man advantage, Junior secured victory when Aguirre struck again in the third minute of stoppage time.
Despite the win, Junior cannot make the Clausura finals as they sit 11th with 22 points, two spots and four points outside the top eight, while Once Caldas (28, +8) remain third behind Santa Fe (28, +10) and Medellin (30, +10).
Once Caldas have lost their past five games in all competitions.
In Neiva, Huila defeated Santa Fe thanks to Juan Fernando Caicedo in the 26th minute, while on Saturday, Medellin gave up a half-time lead when Jhon Valencia struck for Le Equidad in the 58th minute to clinch his team's 11th point from 17 games in the Clausura.
Fourth-placed Deportivo Cali joined Santa Fe and Once Caldas on 28 points after a scoreless draw with Envigado, while Huila sit fifth after notching their fourth win in five games and extending their undefeated streak to 10 matches.
Aguilas Pereira defeated Deportivo Pasto 2-0, while Fortaleza, Patriotas Boyaca and Deportes Tolima all won 1-0 over Atletico Nacional, Boyaca Chico and Alianza Petrolera, respectively.
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