The il replaces le loup.

There is indeed a reference to le sac as well, which is the word qu’, having a direct object function. You can learn more about relative pronouns here for example.

If you want to make sure your instinct is right, you could change the word sac by a feminine word:

En un clin d’œil, le loup les attrapa et les jeta dans une grande caisse qu’il mit sur son dos.