As I heard the story, Simon and Garfunkle first heard Marie Laforet's version of Sur Le Chemin Des Andes, and got it from that. Not necessarily true, just the way I heard it.

I just did some checking. Paul Simon sez "I was in Paris in 1965, right before Simon and Garfunkel broke. I was roaming around Europe by myself, doing folk stuff. It was there I met Los Incas at a concert. I was booked, and they were booked, and that was the first time I had ever heard South American music. They gave me an album of their stuff, and "El Condor Pasa" was on the album. The Simon and Garfunkel record of "El Condor Pasa" was recorded over that preexisting track. So that's where it all comes from, and the notion was, if I liked the music, if it sounded good to me, it was popular. For me there was really no distinction between one culture and another.
from http://www.superseventies.com/sspaulsimon.html

But back to Marie Laforet's song: At the very least, it has been documented that her version predates theirs by about four years.