Miller Bolanos scored a hat-trick as Emelec surrendered the lead then came from behind to beat Sao Paulo 3-2 at Estadio George Capwell in Guayaquil, Ecuador.
Sao Paulo's loss - their first in six games in all competitions - was still enough for the Brazilians to progress to the final four 6-5 on aggregate.
After losing the first leg 4-2 in Brazil last week, Emelec knew they had to make a good start to stand any chance of advancing.
And that is exactly what Emelec did, with Ecuadorian midfielder Bolanos - on loan from LDU Quito - breaking the offside trap before curling the ball past Sao Paulo goalkeeper Rogerio Ceni in the opening minute.
Sao Paulo moved quickly to silence the home crowd, Alan Kardec levelling the scores in the 29th minute via a close-range volley.
Ganso poked the ball over the line from inside the six-yard box five minutes before half-time as Sao Paulo went into the break with a 2-1 lead.
Emelec came out in the second half all guns blazing, Bolanos converting two penalties in the space of four minutes.
Chilean referee Enrique Osses pointed to the spot in the 49th minute following a foul on substitute Marcos Mondaini and Bolanos made no mistake.
Bolanos was at it again four minutes later, completing his hat-trick from the penalty spot after the referee whistled for handball.
Next up for Sao Paulo are Atletico Nacional, who were 1-0 winners over Cesar Vallejo in Peru.
Edwin Cardona's 79th-minute goal gave the Colombians a 2-0 success over two legs.
