Corinthians head Group One with 10 points from four games, three more than Racing of Uruguay.
Independiente Medellin of Colombia are third with three points and Cerro Porteno have one.
Striker Ronaldo poked home a loose ball in the box to give the Brazilian side the lead in the 36th minute at Pacaembu in Sao Paulo.
Captain Chicao curled a free-kick into the top corner just past the hour while left-back Roberto Carlos was voted man of the match for a typically busy performance.
Corinthians were on the back foot in the final stages after midfielder Julio dos Santos pulled one back in the 79th-minute.
Goalkeeper Rafael Santos was forced to make a smart save at the near post from left back Ernesto Cristaldo to preserve his team's lead.
Deportivo Quito retained their chances of qualifying from Group Five with a 1-0 away victory over fellow Ecuadorean side Emelec in the Pacific port city of Guayaquil.
Forward Ivan Hurtado converted a last-minute penalty against 10-man Emelec after a foul by right-back Mariano Mina.
After four matches, Internacional of Brazil lead the group with eight points followed by Uruguay's Cerro and Deportivo both on seven. Emelec, who have no points, are eliminated.
Colombia's Once Caldas, crowned South American champions in 2004, beat Nacional of Paraguay 1-0 at home in Manizales with an early goal by John Jairo Valencia to go top of Group Two.
After five matches, Once Caldas are a point ahead of three times champions Sao Paulo. Monterrey of Mexico are third with six points and eliminated Nacional have none.
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