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.
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.
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.
