That seems to be the distinction, yes. Certainly when people quote both figures the "promedio general" is usually higher than the "promedio académico", and never lower, which makes sense if the latter includes failing grades and the former doesn't. I've seen occasional cases online in which the two figures are the same, which must mean that the person didn't fail any courses.

I've suggested translating the terms literally; you've got to distinguish them somehow and this is probably the least potentially confusing way. After all, the definition of the difference is given in parentheses.

This seems to confirm it:

"Requisitos del postulante: [...] Promedio general mayor de 7,0 (sin aplazos). [...]
Enviar el CV con promedio académico (incluyendo aplazos) y el analítico con las calificaciones obtenidas durante la carrera"
http://www.fbioyf.unr.edu.ar/evirtual/course/view.php?id=185...

For those who don't know what "aplazos" means:

"aplazo.
I. 1. m. Bo, Py, Ar. En el sistema de calificaciones, nota inferior a la mínima requerida para aprobar."
http://lema.rae.es/damer/?key=aplazo

And we've had it before:
https://www.proz.com/kudoz/spanish_to_english/education_peda...

People there used "GPA" for "promedio", but I'm opposed to that. GPA is an American system which has specific characteristics and I don't think it should be used as a generic translation for an average grade.

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Note added at 1 hr (2018-07-14 15:58:30 GMT)
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(By "an American system" I mean "a US system", of course.)