The Argentine attacker was linked with an exit from the Yellow Submarine following their relegation from La Liga in 2011-12, and has signed a five-year deal with his new club.
The 25-year-old striker joined Villarreal from River Plate in January 2008, but struggled to live up to expectations in Spain due to the stiff competition for places.
"When the offer came from a great club like Dynamo I agreed to make the move. I'll be ready to help my team-mates in the next game against Arsenal Kiev," Ruben was quoted as saying by Uefa's official website.
Dynamo Kiev finished last season as runners-up and will enter the Champions League in the third qualifying round.