Nacional are just the second outfit from Paraguay to reach the continental decider - behind three-time champions Olimpia - after losing the semi-final second leg 1-0 away at Uruguay's Defensor.
Substitute Adrian Luna gave the Estadio Centenario hosts hope, when he tapped home in the 55th minute.
However, the second goal Defensor needed to at least force a penalty shoot-out was not forthcoming, as the defensive Nacional successfully protected the lead they gained in the first leg.
Nacional's defence was immediately under pressure in Montevideo, with Defensor earning consecutive corners inside seven minutes - however Gustavo Morinigo's men held firm.
Defensor forward Giorgian De Arrascaeta was dangerous for the hosts, and had the best chance of the opening period - as he latched onto a ball lifted above the Nacional defence, only for his on-target header to be denied by on-rushing goalkeeper Ignacio Don.
Don, however, would be beaten 10 minutes after the interval, as Luna got on the end of a low cross in from De Arrascaeta on the right side of the penalty area.
Despite a flurry of chances - including two shots denied by the woodwork - Defensor could not find the second goal required to force a shoot-out.
Brazilian Felipe Gedoz's effort from range came back off the right-hand upright with just over 20 minutes to play, with Don beaten at full stretch.
Gedoz continued to be dangerous for Fernando Curutchet's men, putting in dangerous balls from the left and even firing a shot from the tightest of angles - which Don would be forced to parry for a corner.
Defender Robert Herrera then had a gilt-edged chance to square the tie, but his shot from point-blank range came back off the crossbar and away to safety.
Nacional will likely play San Lorenzo in the final, with the Argentine outfit leading Bolivar 5-0 heading into their semi-final second leg on Wednesday.
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