With two wins from as many matches, the trio lead the pack – with Atletico top courtesy of a plus five goal difference.
Atletico claimed their second win of the season on Sunday, easily overcoming bottom side Deportivo Cali 3-0.
Fernando Uribe, Juan Valencia and Edwin Cardona struck for Juan Carlos Osorio's Atletico Nacional at Cali's Estadio Olimpico Pascual Guerrero.
Santa Fe sit second – a goal behind – after Silvio Gonzalez's brace led them to a come-from-behind 2-1 win at Fortaleza.
Boyaca Chico made it consecutive 2-1 victories, beating Alianza Petrolera by that scoreline.
Elsewhere, Envigado finished with nine men but still claimed three points in a 4-2 win over Deportes Tolima.
Jonathan Alvarez scored a brace for the victors, while Mateus Uribe struck two late penalties in an eventful affair.
It was Alvarez who opened the scoring in the third minute, beating his man down the left before cutting inside and firing home.
Felipe Noguera levelled for Tolima with a 25-yard free-kick before Alvarez poked in after a fine team move.
But Tolima fought back once more as Charles Monsalvo drilled a penalty down the middle to make it 2-2 on 48 minutes.
That came after Envigado had been reduced to 10 men with Frank Fabra picking up a second yellow card.
Uribe placed in a penalty on 86 minutes before Envigado were down to nine with Yilmar Angulo sent off.
But there was a third spot-kick soon after as Uribe completed the scoring, again going down low to his left.
Medellin were 2-0 winners at home to Deportivo Pasto, Patriotas Boyaca drew 0-0 at home to Once Caldas and Junior and Uniautonoma drew 1-1.
Itagui overcame Atletico Huila 2-1 and La Equidad proved too strong for Millonarios in a 1-0 win.
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