Federer advanced to the fourth round for the 11th straight year with a clinical 6-4, 6-3, 6-2 win on Friday.
Wozniacki joined Romanian Halep and Canadian Bouchard as they all are now eliminated from the tournament.
Simona Halep, last year’s French Open runner’s-up, crashes out 7-5, 6-1 to Mirjana Lucic-Baroni.
Nadal started his French Open campaign with a 6-3 6-3 6-4 win over wildcard Quentin Halys of France.
Federer was in full control against Alejandro Falla and completed a 6-3 6-3 6-4 win in 1st round.
For the first time in the build-up to the tournament Nadal has failed to win a claycourt title in Europe.
The Indian challenge at the second Grand Slam of the season will be led by world number one Sania Mirza in women’s doubles.
Nadal is approaching his 29th birthday and major questions about his form and confidence.
Novak Djokovic seemed to move up a level against Ferrer with a clinical display.
Sania Mirza and Martina Hingis reclaimed the number one spot in the teams ranking.
Nadal beaten 7-6 (7), 6-2 by Wawrinka in the Italian Open quarterfinals on Friday, his fifth loss on clay this season.
During the match, Nadal did not face a single break point and won 90 percent of his first-service points.
After a first-round bye, Nadal opens Wednesday against Turkish qualifier Marsel Ilhan.
Murray continued his remarkable run on clay as he pulled off a stunning upset to dethrone Nadal 6-3 6-2.
Kvitova swept to her 2nd Madrid Open title as she thumped an ailing Kuznetsova 6-1 6-2.