El Fortin set out to stifle their dangerous opponents and managed to secure their spot in the quarter-finals despite a late resurgence from Los Verdolagas
The hosts extended their one-goal aggregate lead when Augusto Fernandez netted early in the second half. They then survived a late scare after Luis Mosquera equalised with a stunning free kick, but it was too little to late for the Colombians as they crashed out of the tournament.
Atletico settled quickly despite a fervent atmosphere and controlled possession for much of the early exchanges.
With 16 minutes on the clock Sebastian Dominguez was fortunate to only receive a booking for a dreadful tackle on Dorlan Pabon, giving away a free kick in a dangerous area. Macnelly Torres delivered it from a central position and Cristian Tula narrowly missed the target with his header.
Four minutes later Marcelo Barovero was called into action, but he dealt with Aviles Hurtado's low drive to the near post easily.
Velez were doing well to contain the Verdolagas, limiting their opportunities to get in behind and penetrate the penalty area.
They became more adventurous as the half continued with Lucas Pratto going twice in quick succession 10 minutes before the break. His first was a rifled volley that flew straight down the middle and he then missed the target with a difficult header from Juan Manuel Martinez's cross moments later.
The hosts continued to grow in confidence and after producing a top-drawer save from Dominguez's header soon after the restart, Gaston Pezzuti was finally beaten in the 53rd minute.
Martinez had provided great width down the left all evening and his pass into Alejandro Cabral created a shooting opportunity. Cabral's cross-goal effort had the beating of the keeper but it bounced back off the post and fortunately Fernandez was on hand to slot home the rebound.
Atletico Nacional were failing to live up to the enthralling performances that they provided during the group stage. However, a moment of individual brilliance was enough to bring them level in the match.
With 20 minutes remaining, Mosquera took a short run-up before curling a perfectly struck free kick into the top corner, well out of the reach of Barovero.
The visitors therefore needed just one goal to progress on the away goals rule and despite an increased level of urgency, Velez remained resolute and held onto the draw.
The Argentine side will now face either Bolivar or Santos in the quarter-final, the second leg of which will be played on Thursday evening.