A packed 40,000 strong Nuevo Gasometro crowd celebrated after Nestor Ortigoza scored the most important goal in the club’s 106-year history with a spot-kick on 36 minutes.
It is the second year in a row that Paraguay have finished runner’s up after Olimpia did so in 2013.
San Lorenzo replied with a long range drive from right back Julio Buffarini that went over the bar, before Nacional midfielder Silvio Torales forced Saints goalkeeper Sebastian Torrico into a difficult save.
San Lorenzo were struggling to find some rhythm in the face of Nacional’s quick counter-attacks but were awarded a penalty in the 36th minute when defender Ramon Coronel handled the ball. Ortigoza made no mistake from the spot, blasting the ball home as Nacional goalkeeper Ignacio Don dived the wrong way.
The home side began finding more space in the second half as Nacional took greater risks at the back in search of an equaliser, with visiting midfielder Marcos Riveros coming close in the 65th minute and striker Fredy Bareiro in the 78th.
“We played a very poor first half, the team were very nervous, tense, they were affected by the expectations of the crowd, but luckily we won,” said San Lorenzo coach Edgardo Bauza.
San Lorenzo, who are famously the club supported by Argentinian born Pope Francis, will represent South America in December’s FIFA Club World Cup.