The 28-year-old, who left Hercules to move to Russia in 2011, managed just three league goals for Rubin last season.
"It has been expensive for us to seal this deal because Nelson is a very popular player at Rubin. For us he's a very important player and will complement the strikers that we already have," Vasquez told reporters.
"Nelson has strength, will and speed, and will also bring goals. We have great confidence in him."
Valdez has scored 12 goals in 59 games for Paraguay.