1978 - Ain't Misbehavin' and On the 20th Century
1981 - 42nd Street and Woman of the Year
1988 - Phantom and Into The Woods
Prior to 1971 sometimes Best Book and/or Score was presented to the Best Musical winner without there being a separate category. It was considered to be a part of the Best Musical award. La Mancha, Cabaret, Hallelujah, Baby!, 1776 and Applause (1966-70) come to mind.
In 1974 Raisin won Best Musical but Candide won Book and Gigi (16 years old at that point) won for Score.
"If my life weren't funny, it would just be true. And that would be unacceptable."
--Carrie Fisher