He took the book . . . . . . . . the shelf and put it . . . . . . . . his bag.

We use 'from' to refer to the place where someone or something starts or originates. Here, the 'shelf' is the place and 'book' is the thing originated. When someone or something comes from outside to the inside, we use the word 'into'. Here, book comes from outside to inside of the bag.