Nadal, the holder of 12 Grand Slam crowns and fresh from his record-breaking eighth French Open triumph in Paris, was seeded behind compatriot David Ferrer who takes the fourth seeding.
Novak Djokovic, Andy Murray and Roger Federer take the top three places.
Wimbledon uses recent grasscourt performances as well as the world rankings to seed players and Nadal was not promoted after he suffered a stunning second-round defeat to Lukas Rosol at the tournament in 2012.
In the women's singles, world number one Serena Williams, the five-time champion, takes top seeding, followed by Victoria Azarenka, the Australian Open champion, with Maria Sharapova, the 2004 Wimbledon winner, named the third seed.