Bolivar substitute Gerardo Yecerotte scored the only goal of the second leg in second-half stoppage time but it meant little as San Lorenzo's 5-0 triumph last week saw the Argentine club progress to the continental final.
It ends a long wait for the Buenos Aires-based club, who became the first club from Argentina to play in the Copa Libertadores in 1960, but are the ninth outfit from their country to reach the competition's decider.
Having crushed Bolivar at home on July 23, San Lorenzo had a huge advantage in their semi-final before Wednesday's second leg in La Paz.
And the margin proved insurmountable for Bolivar, who missed out on the final, just as they did in their previous semi-finals appearance in 1986.
The home side started promisingly at the Estadio Hernando Siles with Carlos Tenorio and Jose Luis Capdevila attempting shots from well outside the penalty area.
But as the half wore on, San Lorenzo started to gain control of the midfield, which saw the visitors' lead striker Nicolas Blandi get into a couple of promising positions without being able to convert.
After the break, Bolivar got on top but were unable to score early enough to have a realistic shot at a comeback with the referee ignoring the hosts' pleas for a penalty on the hour mark, while San Lorenzo goalkeeper Sebastian Torrico made a number of top saves.
In the 92nd minute, Bolivar finally got past Torrico with Yecerotte scoring with an acrobatic volley.
From the resultant kick-off, the home team immediately won the ball back and attacked, with Oscar Rodas flashing a header just wide, but even if the Colombian had scored, San Lorenzo's aggregate lead was too big to be reeled in at such a late stage.
San Lorenzo will take on Paraguay's Nacional Asuncion in the two-legged Libertadores final.
Nacional are set to host the first leg on August 6 before San Lorenzo will welcome the Paraguayans to Buenos Aires a week later.
