Santiago Arzamendia scored in the 1-1 draw away to Uruguayan host Nacional as Cerro Porteno topped the group on goal difference.
Arzamendia opened the scoring with a stunning free-kick on the stroke of half-time in Montevideo but the Paraguayan visitor was pegged back after the break.
Rodrigo Amaral restored parity on the hour-mark with a sensational set-piece of his own to ensure both teams finished on 13 points, though Cerro Porteno topped Group E due to its superior goal difference.
Elsewhere in the group, Atletico Mineiro earned a spot in the Copa Sudamericana thanks to a 2-1 win over as it finished third.
Lucas Pratto's 93rd-minute equaliser saw River earn a 2-2 draw at home to Internacional in Group A.
Already assured of a spot in the knockout round, second-placed River avoided defeat in its final group game with the leader.
Two goals in the space of 15 minutes from Rafael Sobis cancelled out Julian Alvarez's first-half opener for River in Buenos Aires.
But Pratto equalised in the third minute of stoppage time after Internacional goalkeeper Marcelo Lomba made a meal of a cross.
Alianza Lima ended its Group A campaign winless with just one point after a 2-1 defeat at home to Palestino.