League-leading Nacional had Jefferson Duque to thank, with the forward's 53rd-minute goal lifting the hosts to a 1-0 win at the Estadio Atanasio Girardot.
Nacional (+13) are level on 30 points alongside Millonarios (+12) but ahead on goal difference after 15 games, while Junior remain on 27 points.
Juan Carlos Osorio's men went into the match in the midst of a four-game winless streak following three draws and a loss but they returned to winning ways thanks to Duque's first goal since March 2.
Duque was the beneficiary of a short corner, reacting quickest inside the penalty area to guide the ball past helpless goalkeeper Sebastian Viera eight minutes into the second half, ending Junior's five-game winning streak.
Millonarios are hot on the heels of Nacional after they defeated struggling Deportivo Cali 1-0 at the Estadio Nemesio Camacho.
Fabian Vargas' 32nd-minute effort was all that separated the two teams at full time, though the visitors enjoyed a bright start to proceedings without taking full advantage of their opportunities.
Deportivo Pasto were the weekend's big winners, trouncing Atletico Huila 5-1 thanks to a brace from Bosco Frontan.
Pasto scored three goals during the opening 45 minutes before adding another two in the second half as the home side ran riot at the Estadio Departamental Libertad on Saturday.
In other results, Alianza Petrolera made it three wins on the bounce with a 2-0 victory at Uniautonoma.
Camilo Ceballos scored nine minutes after the interval as visiting Itagui accounted for Boyaca Chico 1-0.
Patriotas Boyaca overturned a two-goal deficit to earn a 2-2 draw against Envigado and La Equidad salvaged a point at home to 10-man Fortaleza after Jose Moreno cancelled out Jair Palacios' first-half strike.
Once Caldas and Santa Fe played out a 1-1 stalemate, while Deportes Tolima and Medellin shared the spoils.
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