It marks another milestone in a whirlwind 18 months for the Netherlands-born right back, who ends his five-year association with Dutch outfit.
After graduating from the clubs' academy in 2014, Ebuehi developed into one of the most consistent right-backs in the Eredivisie and made a surprising international switch of allegiance to Nigeria, the country of his fathers birth.
Now after 82 appearances for The Hague, he'll feature in the UEFA Champions League next season with the Portuguese giants, who finished second behind FC Porto this season.
"It is a feeling of great happiness to join a massive club like Benfica," Ebuehi told the club's official website. "It's a dream come true and a big step in my young career.
"Benfica is a great club with excellent facilities and is known all over the world. The fact that the club plays on the big stage was very appealing to me. In fact, it was very easy to choose Benfica."
Ebuehi has played four times for the Super Eagles and is part of Gernot Rohr's 30-man squad for the upcoming FIFA World Cup in Russia.