Fourth-ranked Andy Murray, Andy Roddick, defending champion David Nalbandian and 2006 winner Nikolay Davydenko also made the last eight.
Roddick claimed the sixth spot in the eight-man Masters Cup in Shanghai next month, leaving Juan Martin del Potro and Gilles Simon waiting on Friday's results to see if they keep the last two berths.
Nadal beat Gael Monfils of France 6-3, 6-2, Federer defeated Marin Cilic of Croatia 6-3, 6-4, while Djokovic, the year's other major winner, lost to Jo-Wilfried Tsonga of France 6-4, 1-6, 6-3.
Nadal saved all nine break points he faced and broke Monfils three times, clinching victory on his first match point when the Frenchman hit a forehand wide.
"I'm not playing my best level, but I'm not playing badly,'' Nadal said. "If I can improve a bit for tomorrow and for Shanghai I think I can finish the year playing well.''
Nadal will play Davydenko, who crushed 2005 champion Tomas Berdych of the Czech Republic 6-1, 6-1.
Even though Nadal was guaranteed to start 2009 ahead of Federer in the rankings, he feels like he's still behind him.
"Roger had four or five years with the No. 1, winning two, three Grand Slams a year,'' Nadal said. "So for that reason I think everybody says Federer is the best.''
Federer's fourth ace sealed a dominant win over 20-year-old Cilic, and allowed him to cast an eye on his first semifinals at Bercy Indoor Arena.
"I prefer to come back to a place where I had success in the past. This is not the case here,'' Federer.
He'll have to go through James Blake, who defeated Philipp Kohlschreiber of Germany 6-4, 6-4.
Federer is 8-1 against Blake, with the Swiss star's only loss in the quarterfinals at the Beijing Olympics in August.
"I'm not the revengeful type, but I would be pleased to beat him,'' Federer said.
Djokovic beat Tsonga in the Australian Open final for his first major title, but has lost to the Frenchman in successive matches since then. The latest defeat made the world No. 3 less of a fan of the indoor carpet.
"I just don't feel quite comfortable on the court,'' the Serb said. "When you play indoors, points get quicker. (Tsonga) was serving really well.''
Tsonga will next meet Roddick for the first time in nearly two years.
"If I manage to stay in shape physically, I will go from strength to strength in this tournament,'' Tsonga said.
The seventh-seeded Roddick overcame 10th-seeded Simon 6-3, 7-5 on his fifth match point. Both have won three titles this year.
"It wasn't going to do me any good to play patty-cake back and forth with him today,'' Roddick said. "I'm not as quick as he is and I'm not as consistent as he is. It actually made for a pretty simple game plan.''
Murray topped Fernando Verdasco of Spain 6-3, 7-6 (6) for his 14th straight win, staying on track for a third straight Masters title.
Murray will face Nalbandian in the quarterfinals, after the Argentine defeated countryman del Potro 6-4, 6-0.
"His results have been pretty special the last couple of years. Should be a great match,'' Murray said of Nalbandian. "He picks his schedule very well and is fresher than the other players toward the end of the year.''
After victories at Cincinnati and Madrid, Murray hopes to become the only player to win three straight Masters titles.
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Federer, Roddick in Paris quarters
Roddick reaches Paris quarters
