The banned substances bethamethosone and methylprednisolone, both steroid related, were detected in a drugs test carried out after an Intertoto Cup match against Atletico Madrid on August 24.
Senna was suspended provisionally by UEFA on October 21 and the 60-day ban will run from that date. He will miss another seven league matches and two UEFA Cup games during the remainder of his ban, which will expire on December 20.
Senna, 28, joined Villarreal from Sao Caetano in Brazil in 2002. He played only 25 games over his first two seasons in Spain but he had been ever-present for Villarreal until his suspension.