Federer's 6-4, 6-4 victory over South African Kevin Anderson was enough to secure his spot at the World Tour Finals in London, his 12th straight appearance at the season's glamour finale.
"It's magnificent to come back to Paris which is close to my heart especially after 2009 (his only French Open triumph) and 2011," when he won the Paris Masters," said Federer.
"I'm just happy right now to have made it again, you know," the Basel native said.
"It's definitely somewhat of a highlight of the season for me after having a tough few months to still make it to the World Tour Finals," he said.
"It's a good moment right now sitting here knowing it's secure." added the Swiss former world number one.
Swiss number two Stanislas Wawrinka increased his chances of protecting his eighth-place ranking when he ground down Spaniard Feliciano Lopez 6-3, 3-6, 6-3.
This year's US Open semi-finalist now faces 13th seed Nicolas Almagro following the Spaniard's comfortable 6-4, 6-3 victory over Croatian Ivan Dodig.
At a packed Bercy arena, Nadal turned in a trademark swashbuckling display to defeat Spanish compatriot Marcel Granollers 7-5, 7-5.
Nadal, 27, hasn't played at the Paris tournament since 2009 and is attempting to become the first player since Andre Agassi in 1999 to win both the French Open and Paris Masters in the same year.
Nadal advances to a last-16 meeting against last year's surprise finalist Jerzy Janowicz.
The eight-time French Open winner, who is chasing a record sixth Masters title in the same season, said after the match he was happy to win but needs to improve.
"It can be difficult when your opponent serves well and you didn't play your best, so matches are very close, especially on a surface like this one," Nadal said.
"I didn't play well tonight," he said.
"Something that can happen after two weeks without playing and after a long time without playing on indoors, this kind of surface.
"I have to improve a lot for Thursday."
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Philipp Kohlschreiber will be Federer's next opponent after the experienced German blew away two-time Paris semi-finalist and compatriot Tommy Haas 6-2, 6-2.
Defending champion David Ferrer of Spain was pushed to three sets by Czech Lukas Rosol in his opening match before easing into the last-16, 6-0, 2-6, 6-3.
The experience of the 31-year-old French Open runner-up proved decisive in the decider as Ferrer consistently put pressure on the Rosol serve and was rewarded with a third-round tie against Frenchman Gilles Simon.
Argentine fourth seed Juan Martin Del Potro made it 14 wins from 15 matches since the US Open as he defeated Marin Cilic.
The 25-year-old, who won his fourth ATP title of the year last weekend at Basel, withstood 19 aces from his opponent before closing out a tense encounter 6-4, 7-6 (7/3) against the Croatian.
Del Potro, who is playing what he said 'is the best tennis of my life', will next face dangerous Bulgarian Grigor Dimitrov.
Earlier, big-serving American John Isner bombarded Polish qualifier Michal Przysiezny with 27 aces on the way to a 7-6 (7/3), 4-6, 6-3 second-round win and a third round matchup against Novak Djokovic.
In the final match of the day, Canada's Milos Raonic kept his outside chances of qualifying for London flickering, with a ruthless 6-3, 6-4 thrashing of Robin Haase, from the Netherlands.