Fernandez strained his left knee during practice on Oct. 30. It's the same knee he injured last January, ending his season with the Minnesota Wild. The Bruins gave no timetable for his return.
Thornton broke a bone in his left foot and is expected to miss four to six weeks.
Boston traded forward Petr Kalus and a fourth-round draft pick to Minnesota for Fernandez in July. He has a 2-2 record and a 3.93 goals-against average in four games this season.
Thornton has played in 13 games this season after joining Boston as an unrestricted free agent in the offseason. In 2006-07, he had two goals in 48 games for the Anaheim Ducks and four goals in 15 games for AHL Portland.
The Bruins also recalled defensemen Matt Lashoff and Matt Hunwick from AHL Providence.