Only two points separated Bolivar, Leon, Flamengo and Emelec heading into the final matchday in Group Seven.
But Xabier Azkargorta's Bolivar led from start to finish accounting for Emelec 2-1, while Leon left it late as they overcame Flamengo 3-2.
Victory ensured the Bolivians topped the group on 11 points to progress to the next round of South America's continental competition, one point ahead of Mexico's Leon.
Flamengo of Brazil finished on seven points, with Ecuador's Emelec one point adrift.
With the group going down to the wire, Bolivar needed to make a bright start at the Estadio Hernando Siles and they did courtesy of William Ferreira, who opened the scoring in the second minute.
Juanmi Callejon gave the hosts some breathing space six minutes into the second half, though there were a few nervy moments when Luis Escalada pulled a goal back with two minutes remaining.
Over at the Estadio do Maracana in Brazil, fans were treated to a five-goal thriller.
Leon led twice inside the opening 31 minutes thanks to Franco Arizala and former Wigan striker Mauro Boselli, but Flamengo hit back with goals from Andre Santos and Alecsandro.
But as the game petered out for a draw, Carlos Pena popped up to score the match-winning goal in the 84th minute, sending a dagger through the hearts of the Brazilians.
Elsewhere on Wednesday, a four-goal haul from Daniel Angulo was not enough to send Independiente del Valle through to the next round.
Angulo's man-of-the-match performance inspired the Ecuadorians to a come-from-behind 5-4 victory over Chile's Union Espanola, who still topped Group Two on nine points.
Independiente (+0) finished level on eight points with second-placed Argentine side San Lorenzo (+1), who cruised past Brazil's Botafogo 3-0, but adrift on goal difference.
Botafogo crashed out of the competition on seven points.
In Group Five, Cruzeiro advanced as Universidad Chile could only draw 1-1 with Uruguayan leaders Defensor Sporting.
Three first-half goals saw the Brazilians run out 3-0 winners at home to bottom side Real Garcilaso of Peru.
Cruzeiro (+6) finished on 10 points alongside Universidad (-3) but their superior goal difference saw them take second spot behind Defensor, who had 11 points after six games.
