The 28-year-old, who has won over 20 caps, leaves as part of a clearout at the club known as the 'Yellow Submarine' after they were relegated from La Liga in May.
Villarreal finished fourth in 2011 and began the last campaign in the Champions League before sliding down the table and being relegated after losing on the final day of the season.
Nilmar joins players like Spain goalkeeper Diego Lopez, Ecuador winger Jefferson Montero and Argentine striker Marco Ruben in leaving the club with the exits of high-profile players forced upon Villarreal by their changed circumstances.
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