Spanish third seed Nadal, chasing an unprecedented eighth Paris title, saw off Slovakia´s Martin Klizan 4-6, 6-3, 6-3, 6-3 to record his 54th win in 55 matches at the tournament.[break]
For the second round in succession, the 26-year-old dropped the first set as he struggled in the cold, heavy conditions where the temperature just crept over the 12-degree mark.
He then launched a blistering attack on tournament chiefs who he described as a "joke" and claimed he was being treated unfairly.
Nadal´s match had been held over from Thursday after torrential rain swamped Paris.
He had been placed third on the Court Suzanne Lenglan schedule, following one men´s match and a women´s singles.
His third round opponent, Fabio Fognini, meanwhile, had been scheduled second on Court Three to follow just one women´s singles match which took only an hour to complete.
"The schedule was wrong, it was a bad decision," said Nadal.
Nadal was further incensed when he was told that Fognini had been given an earlier start time because he and opponent Lukas Rosol had doubles to play later together in the day.
"Today I was playing three hours while my opponent was in the locker room watching TV," said Nadal.
"I cannot play third when my opponent has played second. The excuse they gave me was that they had to play doubles, but that´s a joke. In that case I should sign up for doubles."
With third seed Nadal having to play his third round match on Saturday, second seed Federer has already ensured his place in the last 16.
His 6-3, 6-4, 7-5 win over France´s 30th seed Julien Benneteau marked his best start to the tournament.
As well as racking up his 57th win in Paris -- just one behind the record of 58 held by Guillermo Vilas and Nicola Pietrangeli -- the 31-year-old has made the fourth round in record time.
He has dropped just 23 games in three rounds compared to 24 in 2007 and 27 in 2010.
Federer, the 2009 champion, next faces Gilles Simon, the 15th-seeded Frenchman who beat American 18th seed Sam Querrey 2-6, 6-3, 2-6, 7-6 (7/2), 6-2.
Federer has a 3-2 record over Simon, beating him in Rome two weeks ago in their only meeting on clay.
The 17-time major winner said that Nadal had just been unlucky with the scheduling.
"I understand the frustration, but it´s complicated. Fifty percent of players couldn´t complete their matches on Thursday," said the Swiss.
Spanish fourth seed David Ferrer, who made the semi-finals in 2012, continued his low-key run, beating compatriot Feliciano Lopez, 6-1, 7-5, 6-4, to set-up a fourth round clash against Kevin Anderson.
The 23rd seed became the first South African to reach the fourth round since Wayne Ferreira in 1996 when he knocked out Canadian 14th seed Milos Raonic, 7-5, 7-6 (7/4), 6-3.
French wildcard Gael Monfils, who had shocked fifth seed Tomas Berdych in the first round, squandered four match points before going down to Tommy Robredo.
The Spanish veteran missed the 2011 and 2012 tournaments due to a leg injury and saw his world ranking plummet to 471.
But the 31-year-old, a four-time quarter-finalist, turned back the clock to win 2-6, 6-7 (5/7), 6-2, 7-6 (7/3), 6-2.
He will meet compatriot, 11th-seeded Nicolas Almagro, for a quarter-final place.
Croatia´s 10th seed Marin Cilic was the biggest casualty, losing 7-6 (14/12), 6-4, 7-5 to Serbia´s Viktor Troicki.
Troicki will next face Jo-Wilfried Tsonga, regarded as France´s best hope of a first men´s champion since Yannick Noah in 1983.
Sixth-seeded Tsonga defeated Jeremy Chardy, 6-1, 6-2, 7-5.
In delayed second round matches, French seventh seed Richard Gasquet made the last 32 for the third successive year with a 6-3, 6-3, 6-0 win over Polish qualifer Michal Przysiezny.
German 12th seed Tommy Haas ended the run of American qualifier Jack Sock, 7-6 (7/3), 6-2, 7-5.
Haas, playing in his 52nd Grand Slam event, is the first 35-year-old to reach the third round in Paris since Jonas Bjorkman in 2007.
French Open results on Friday
Men
3rd rd
Tommy Robredo (ESP x32) bt Gael Monfils (FRA) 2-6, 6-7 (5/7), 6-2, 7-6 (7/3), 6-2
Nicolas Almagro (ESP 11) bt Andreas Seppi (ITA x20) 7-6 (7/1), 6-0, 6-4.
Kevin Anderson (RSA x23) bt Milos Raonic (CAN x14) 7-5, 7-6 (7/4), 6-3
David Ferrer (ESP x4) bt Feliciano Lopez (ESP) 6-1, 7-5, 6-4
Jo-Wilfried Tsonga (FRA x6) bt Jeremy Chardy (FRA x25) 6-1, 6-2, 7-5
Viktor Troicki (SRB) bt Marin Cilic (CRO x10) 7-6 (14/12), 6-4, 7-5
Gilles Simon (FRA x15) bt Sam Querrey (USA x18) 2-6, 6-3, 2-6, 7-6 (7/2), 6-2
Roger Federer (SUI x2) bt Julien Benneteau (FRA x30) 6-3, 6-4, 7-5
2nd rd
Rafael Nadal (ESP x3) bt Martin Klizan (SVK) 4-6, 6-3, 6-3, 6-3
Tommy Haas (GER x12) bt Jack Sock (USA) 7-6 (7/3), 6-2, 7-5
Mikhail Youzhny (RUS x29) bt Federico Del Bonis (ARG) 6-3, 6-7 (5/7), 7-5, 6-4
Jerzy Janowicz (POL x21) bt Robin Haase (NED) 6-4, 4-6, 6-4, 6-3
Nikolay Davydenko (RUS) bt Denis Istomin (UZB) 6-4, 7-5, 6-2
Richard Gasquet (FRA x7) bt Michal Przysiezny (POL) 6-3, 6-3, 6-0
John Isner (USA x19) bt Ryan Harrison (USA) 5-7, 6-7 (7/9), 6-3, 6-1, 8-6
Stanislas Wawrinka (SUI x9) bt Horacio Zeballos (ARG) 6-2, 7-6 (7/2), 6-4
Janko Tipsarevic (SRB x8) bt Fernando Verdasco (ESP) 7-6 (7/3), 6-1, 3-6, 5-7, 8-6
Women
3rd rd
Serena Williams (USA x1) bt Sorana Cirstea (ROM x26) 6-0, 6-2
Roberta Vinci (ITA x15) bt Petra Cetkovská (CZE) 6-1, 2-6, 6-2
Angelique Kerber (GER x8) bt Varvara Lepchenko (USA x29) 6-4, 6-7 (3/7), 6-4
Ana Ivanovic (SRB x14) bt Virginie Razzano (FRA) 6-3, 6-2
Carla Suárez (ESP x20) bt Mónica Puig (PUR) 6-4, 7-5
Sara Errani (ITA x5) bt Sabine Lisicki (GER x32) 6-0, 6-4
2nd rd
Stefanie Voegele (SUI) bt Kaia Kanepi (EST) 7-6 (8/6), 3-6, 8-6
Maria Kirilenko (RUS x12) bt Ashleigh Barty (AUS) 6-3, 6-1
Marion Bartoli (FRA x13) bt Mariana Duque (COL) 7-6 (7/5), 7-5
Francesca Schiavone (ITA) bt Kirsten Flipkens (BEL x21) 6-1, 4-6, 6-3
Maria Sharapova (RUS x2) bt Eugénie Bouchard (CAN) 6-2, 6-4
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