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.
San Lorenzo’s win ends a five-year Brazilian stranglehold on the trophy, and means they are the last of Argentina’s ‘big five’ to win the continent’s top club honour.
It is the second year in a row that Paraguay have finished runner’s up after Olimpia did so in 2013.
Nacional started brightly and came close in the first minute when San Lorenzo midfielder Juan Mercier lost the ball inside the box and Derlis Orue fired against the post.
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 goal gave San Lorenzo the impetus and they pinned Nacional back for the remainder of the first half.
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.