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.
Swim Week Miami Beach 2014 [PHOTOS]