Boca moved through to the knockout round as Group G winner after edging 10-man Paranaense 2-1 in Buenos Aires on Friday (NZST).
Beaten by bitter rival River Plate in last season's decider, Boca was in danger of missing out on the last 16 after Marco Ruben's 66th-minute opener.
Boca's Lisandro Lopez, however, equalised six minutes later with a close-range effort on matchday six La Bombonera.
Paranaense was reduced to 10 men in the 80th minute after Wellington's red card and substitute Carlos Tevez sealed Boca's progress in the fifth minute of stoppage time.
The result saw Boca finish with 11 points, two ahead of Brazilian side Paranaense and three clear of Deportes Lima – which defeated Jorge Wilstermann 2-0.
In Group C, Godoy Cruz joined fellow Argentine side Boca in the next round thanks to its 1-0 win over Universidad Concepcion.
Godoy Cruz finished on nine points, level with leader Olimpia but adrift on goal difference after the latter lost 1-0 at home to Sporting Cristal.
Sporting Cristal earned seven points from six games to claim third, a point ahead of Concepcion.