The reigning champions came from behind to beat Envigado 2-1 in their quarter-final second leg on Sunday with Francisco Najera and Juan Pablo Angel scoring the goals for Nacional.
The win saw Nacional join Santa Fe, Junior and Millonarios in the final four of the Colombian Apertura campaign.
Envigado travelled to Medellin knowing they would have to start strongly to reel in the home side's 4-1 lead from the first leg last week and the visitors' coach Juan Carlos Sanchez would have been thrilled when Favio Burbano opened the scoring in the third minute.
Burbano finished from near the penalty spot after being teed up by Jonathan Alvarez but Envigado could not build on that early momentum.
In the 72nd minute, Nacional effectively ended the contest when Najera lifted the ball over visiting goalkeeper Victor Soto from close range, following Edwin Cardona's right-wing cross.
Angel capped off the hosts' triumph three minutes, converting after Soto fumbled another cross from Cardona.
In Sunday's other quarter-final, Santa Fe lost 2-1 to Once Caldas but triumphed 5-3 on aggregate.
On Saturday, Junior survived going down to 10 men in the opening half hour to advance 3-2 on aggregate.
Junior's Juan Dominguez was shown a red card in the 27th minute and Itagui took advantage seven minutes later to edge 2-1 ahead on aggregate when Leonardo Castro scored.
But Edison Toloza saved Junior with a second-half brace, scoring the equaliser just before the hour mark and then converting a 79th-minute penalty to send his team into the final four.
In the other quarter-final, Millonarios prevailed 2-1 on aggregate against La Equidad after a 1-1 draw in the second leg.
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