The result followed a 1-0 win to Guarani in last week's first leg in Asuncion and the Paraguayan club advanced by virtue of having scored an away goal.
Corinthians looked set to clinch a place in the third and final qualifying round when Luan and Mauro Boselli gave them an early 2-0 lead here.
However, the hosts suffered a major blow when Pedrinho was sent off after picking up a second yellow card for a bad foul on the half hour mark.
Despite their numerical advantage, Guarani struggled to create clear scoring chances against a resolute Corinthians defence. However the vital away goal came courtesy of a curling Fernando Fernandez free-kick just after halftime.
In other second-round qualifiers on Thursday, Cerro Porteno beat Universitario 1-0 and 2-1 on aggregate, Palestino routed Cerro Largo 5-1 to complete a 6-2 overall win and Argentina's Atletico Tucuman beat Bolivia's The Stongest on penalties after the teams were locked at 2-2 overall.