Fernando Jubero's Guarani drew 1-1 at Sporting Cristal on the final matchday in Group Eight, simultaneously clinching second spot in the standings and denying their Peruvian hosts a berth in the knockout stages.
The win took Guarani to nine points, three adrift of Group Eight-leaders Racing Club, who defeated Deportivo Tachira 3-2, while Sporting were left in third on seven.
Having scored Guarani's equaliser in a 2-2 draw with Sporting in Paraguay in February, Federico Santander haunted the Peruvian club again on Tuesday, scoring the opening goal for Jubero's side.
A teasing cross from Julian Benitez found Santander in the 14th minute and the 23-year-old striker poked the ball into the net from the edge of the six-yard box.
While Sergio Blanco equalised for the home team just before the hour-mark with a diving header, Sporting could not fashion the winning goal they needed to qualify for the round of 16.
In Group Three, Huracan kept their round-of-16 hopes alive with a 3-1 win over Cruzeiro in Argentina.
The Brazilian club had arrived in Buenos Aires with two wins and two draws from their first four matches of the 2015 Copa Libertadores but they were two goals down within the opening half-hour thanks to Ramon Abila.
The Huracan forward struck in the 15th and 26th minutes - coolly beating Cruzeiro goalkeeper Fabio before converting from Edson Puch's cut-back.
Cruzeiro hit back through a penalty from Leandro Damiao in the 61st minute but Federico Mancinelli wrapped up Huracan's win two minutes later with a header from a set-piece.
Huracan's triumph allowed Club Universitario (nine points) to claim top spot in Group Three with a 2-0 victory over bottom club Mineros de Guayana (one).
Universitario's win came after their Bolivian league match was abandoned on Saturday due to an insufficient number of players on the field.
Only seven youth-team players - the minimum required - were named in Universitario's starting XI at Bolivar in protest to fixture congestion and the match lasted just 13 minutes following an injury.
Cruzeiro (eight) remain second with one game remaining, with Huracan (seven) close behind.
