A goalless draw in Buenos Aires was enough to send Guarani through to the semi-finals at the expense of 10-man Racing Club.
Guarani took a narrow lead to the Argentine capital after claiming a late 1-0 win in the opening leg of their quarter-final tie in Paraguay last week.
And Julian Benitez's 85th-minute strike was all that separated the two teams following Thursday's stalemate at Estadio Presidente Juan Domingo Peron as Guarani set up a final-four showdown with River Plate, though the game was not without its moments.
Racing striker Gustavo Bou put the ball in the back of the net in the 14th minute, however his effort was ruled out for offside.
Guarani were unfortunate not to extend their aggregate lead on the stroke of half-time after Racing goalkeeper Sebastian Saja saw red.
Saja was sent off for tripping Marcelo Palau, who pounced on a misplaced back pass, but substitute keeper Nelson Ibanez produced a fine save at full stretch to deny Benitez from the spot.
Guarani will travel to River for the first leg of their semi-final on July 15.
