While I realize it is stretching it a bit to refer to Secretary of Defense nominee Robert Gates as an 'academic', he does qualify in some ways since he is as a history Ph.D. and the president of a university. After a little checking, I discovered that previous Secretaries of Defense fit the mold of an academic even better than Gates.
First was James Schlesinger, a Ph.D. in economics who taught at the University of Virginia, before serving as Secretary of Defense under Nixon from 1973-1975.
Second, Harold Brown, a Physics Ph.D., who had only a short teaching stint, but eventually ended up as Jimmy Carter's Secretary of Defense from 1977-1981.
Third was Les Aspin, a Ph.D. in economics (and a BA in history), who taught for several years at Marquette. He was Clinton's Secretary of Defense from 1993-1994.
William Perry, Bill Clinton's Secretary of Defense from 1994-1997, had a Ph.D. in math. However, as far as I could tell, he never had an academic appointment.