Copa Sudamericana champions Sao Paulo were 8-4 aggregate winners having gone into the second leg with a 5-0 advantage, while Gremio beat Liga on penalties.
Ney Franco's Sao Paulo progressed despite a 4-3 defeat in Bolivia, at 3,600metres above sea level in La Paz city.
Sao Paulo took a very early lead with Luis Fabiano heading home two minutes after kick-off, and managed to take a three-goal lead at the Estadio Hernando Siles as Jadson made it 2-0 at the 15th and Osvaldo added another 11 minutes before half-time.
With an eight-goal advantage in the tie, Sao Paulo relaxed and Bolivar put on a show for their fans.
William Ferreira reduced the deficit in the 37th minute and Nelson Cabrera netted a brace to equalise.
In the 58th minute, Cabrera headed a Gerardo Yecerotte cross from the right and he then levelled the game on the night with a free-kick. After 74 minutes, Ferreira gave Bolivar a consolation win with a penalty.
Ney Franco said: "We failed a lot technically. We lost our focus on the game and we paid with a loss."
Sao Paulo will go into Group Three alongside compatriots Atletico Mineiro, Bolivian side The Strongest and Arsenal of Argentina.
Gremio, meanwhile, defeated Liga Deportiva 1-0 at home in Porto Alegre and won 5-4 on penalties, as Liga had claimed a 1-0 win in Quito last week.
Elano netted the goal that levelled the tie at the Arena do Gremio stadium in the 62nd minute, with a great right-foot strike, while Liga ended the game with 10 men as defender Koob Hurtado was sent off in the 88th minute due to a bad challenge on Jean Deretti.
In the shoot-out, Gremio keeper Marcelo Grohe saved Eduardo Morante's shot and put the Brazilian team into Group Eight, where the will tackle Brazilian champions Fluminense, Venezuela's Caracas and Huachipato of Chile.