While their relegation from the Brazil Serie A is all but confirmed, Ponte Preta's fine cup run continued thanks to the 4-2 aggregate win.
Leonardo put them further ahead in the tie with a 43rd-minute opener at the Estadio Romildo Vitor Gomes Ferreira.
Luis Fabiano levelled the second leg with six minutes remaining but Sao Paulo, mid-table in the Serie A, were never going to overhaul the deficit.
Ponte Preta, who have never won the Copa Sudamericana, will face either Paraguayan outfit Libertad or Argentina's Lanus in the final.
Leonardo pounced on a poor clearance to open the scoring two minutes before the break, putting away his chance on the second effort after his initial strike was blocked.
Substitute Luis Fabiano pulled a goal back for Sao Paulo but Ponte Preta cruised to book their place in the final for the first time.
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