Mallorca-born Llagostera Vives, 33, gave a urine sample at the Bank of the West Classic in Stanford in July where she was competing in the doubles, the ITF said.
After analysis at the WADA-accredited laboratory in Montreal, Canada it was found to contain the prohibited substance.
"An independent hearing was held (on Oct. 29), in which Ms Llagostera Vives ... was not able to demonstrate how the d-amphetamine entered her system," the ITF added.
"It was determined that she is suspended from participation for a period of two years, commencing from 8 September 2013, the date on which she was provisionally suspended, and so ending at midnight on 7 September 2015."
Llagostera, who has two career singles and 16 doubles titles, denied deliberately doping and suggested to the tribunal she may have inadvertently ingested d-methamphetamine by drinking from the wrong water bottle while training.