Djokovic, in an early match, rallied for a 4-6, 6-2, 6-3 victory over 14th-seeed Juan Monaco in nearly 2 1/2 hours. The Serb, however, faced just one break point after the first set.
Federer, in Thursday's final match, got past Juan Carlos Ferrero, the 2003 French Open champion, 6-2, 5-7, 6-1. Federer won 74 percent of the points on serve, with his lone service break costing him the second set. But he lost only 12 points -- four on serve -- in sweeping through the third set.
World No. 3 -- but second seed -- Rafael Nadal blitzed Marcel Granollers 6-1, 6-1 behind five breaks in seven receiving games.
But fourth-seeded Andy Murray was eliminated by 16th-seeded Richard Gasquet 6-7 (1-7), 6-3, 6-2. The match took 3 hours and turned on Gasquet's five breaks over the last two sets.
Also Thursday, fifth-seeded Jo-Wilfried Tsonga stopped 10th-seeded Juan Martin del Potro 6-4, 6-1; No. 6 David Ferrer beat Gilles Simon 6-0, 7-6 (7-5); and seventh-seeded Tomas Berdych ousted Nicolas Almagro 7-6 (7-3), 6-3.
Andreas Seppi became the only unseeded player to reach the quarterfinals, beating Stanislas Wawrinka 6-7 (1-7), 7-6 (8-6), 7-6 (8-6), in a 3-hour, 21-minute marathon.
Seppi takes on Federer in the quarterfinals and Djokovic draws Tsonga. Nadal is to play Berdych and Ferrer faces Gasquet in the other matches Friday.