“Our analysis shows that the two voices are similar but likely not identical,” Berisha said.

They also point out the main differences between the two voices in the paragraphs below this quote. I do believe that they hired a voice actress and that they didn’t train on SJ’s voice, or at least not entirely. However, I wouldn’t be surprised if there was big push for finding a voice similar to SJ’s voice in Her, no matter how much they deny this.