I might say Spirited Away is a good example. I don’t know how many Ghibli films are based on books if at all, but that one in particular fits the bill.
On a similar vein, many western animated films are not based on a book. Examples that come into mind are The Incredibles and Toy Story (Pixar), Lilo and Stitch (Disney), On the Road to El Dorado (DreamWorks). I’m sure there’s more…