For both UCs and CSUs, passing a precalculus course validates a deficient grade (D or F) in geometry. For UC, it is the omission of geometry that cannot be validated.
http://admission.universityofcalifornia.edu/counselors/files/validation_matrix_math_lote.pdf
Fortunately, the D grade in 9th grade does not become part of your UC or CSU calculated GPA.
What campuses and majors did you apply to? If you are a California resident with a 3.3 GPA, you should be admitted to non-impacted majors at non-impacted CSU campuses. See http://www.calstate.edu/sas/impactioninfo.shtml to find out what majors and campuses are impacted. For impacted majors and/or campuses, it depends on how impacted they are.