Confirmation came from tournament organisers on Wednesday, after Nadal had pre-empted their announcement by speaking out to express his dissatisfaction at the move.
For the grass-court grand slam that starts next Monday, eight-time champion Federer will be the second seed and two-time winner Nadal the third seed, reversing their positions in the ATP standings.
Wimbledon formulates its men's singles seedings based on world rankings and grass-court results over the last two years, and on the latter basis Federer has a better record than the Spaniard.
French Open champion Nadal told Movistar Plus on Tuesday he would accept Wimbledon's decision, but he added: "The only thing that does not seem right to me about this story is that it is only Wimbledon that does it, only one tournament.
"It has not only happened to me, it has happened to other players. They do not respect the status that some players have earned throughout the season."
— Roger Federer (@rogerfederer) June 25, 2019
Nadal reached the semi-finals at Wimbledon last year, losing a five-set classic to Novak Djokovic, his best performance since losing in the 2011 final.
Djokovic, the world number one, is the men's top seed. The player he beat in last year's final, South African Kevin Anderson, is boosted from his world ranking of number eight to become the fourth seed.
The women's seedings are not determined by the same formula as the men's event, and they show no deviation from the world rankings, with Australia's French Open winner Ashleigh Barty at number one, followed by Japan's Naomi Osaka, Czech Karolina Pliskova and Dutch player Kiki Bertens.
Defending champion Angelique Kerber is the fifth seed and seven-time winner Serena Williams the 11th seed. Injured Canadian player Bianca Andreescu is the only player from the top 32 absent from the list, allowing world number 33 Lesia Tsurenko to take a seeding.
Men's seeds: 1 Novak Djokovic, 2 Roger Federer, 3 Rafael Nadal, 4 Kevin Anderson, 5 Dominic Thiem, 6 Alexander Zverev, 7 Stefanos Tsitsipas, 8 Kei Nishikori, 9 John Isner, 10 Karen Khachanov, 11 Daniil Medvedev, 12 Fabio Fognini, 13 Marin Cilic, 14 Borna Coric, 15 Milos Raonic, 16 Gael Monfils, 17 Matteo Berrettini, 18 Nikoloz Basilashvili, 19 Felix Auger-Aliassime, 20 Gilles Simon, 21 David Goffin, 22 Stan Wawrinka, 23 Roberto Bautista Agut, 24 Diego Schwartzman, 25 Alex De Minaur, 26 Guido Pella, 27 Lucas Pouille, 28 Benoit Paire, 29 Denis Shapovalov, 30 Kyle Edmund, 31 Laslo Djere, 32 Dusan Lajovic.
Women's seeds: 1 Ashleigh Barty, 2 Naomi Osaka, 3 Karolina Pliskova, 4 Kiki Bertens, 5 Angelique Kerber, 6 Petra Kvitova, 7 Simona Halep, 8 Elina Svitolina, 9 Sloane Stephens, 10 Aryna Sabalenka, 11 Serena Williams, 12 Anastasija Sevastova, 13 Belinda Bencic, 14 Caroline Wozniacki, 15 Wang Qiang, 16 Marketa Vondrousova, 17 Madison Keys, 18 Julia Goerges, 19 Johanna Konta, 20 Anett Kontaveit, 21 Elise Mertens, 22 Donna Vekic, 23 Caroline Garcia, 24 Petra Martic, 25 Amanda Anisimova, 26 Garbine Muguruza, 27 Sofia Kenin, 28 Hsieh Su-wei, 29 Daria Kasatkina, 30 Carla Suarez Navarro, 31 Maria Sakkari, 32 Lesia Tsurenko.
Photo Getty Images. Caption: Roger Federer has been handed a Wimbledon boost