The top-seeded/world No. 1 Federer was leading Robin Soderling 6-4, 3-0 when the Swede complained of illness and quit in the second set.
Federer, the reigning Wimbledon and U.S. Open champion, won this Miami tournament in 2005 and 2006.
Federer's fourth-round opponent will be Argentine slugger Jose Acasuso, who beat Israeli Dudi Sela 6-4, 6-4.
Fourth-seeded Russian Nikolay Davydenko came from behind to beat Italian Simone Bolelli 6-7 (5-7), 7-5, 6-1; Julien Benneteau beat fellow Frenchman Jo- Wilfried Tsonga 6-3, 6-3; and Serbian Janko Tipsarevic defeated former Australian Open champion Thomas Johansson of Sweden 6-4, 6-4.