The Paraguayan striker will move to Mestalla upon the completion of a medical, after spending a season with the Russian Premier League outfit
The Paraguayan left La Liga a year ago, but after an ineffective season in the Russian Premier League he has made a swift return to Spain.
Sporting director Braulio Vazquez was delighted to have struck a deal for the 28-year-old, who had previously represented Borussia Dortmund and Werder Bremen.
"It has been expensive for us to seal this deal because Nelson is a very popular player at Rubin," he told the club's official website.
"For us he's a very important player and will complement the strikers that we already have. Nelson has strength, will and speed, and will also bring goals.
"We have great confidence in him."