The city on Tuesday passed a ban on the sale of cats and dogs from commercial breeders.
The "humane ordinance" goes into effect next year.
Pet stores will only be able to sell dogs and cats obtained from a humane society, or an animal rescue group.
Supporters say the move will help put puppy mills that abuse animals out of business.
Naperville is the 341st municipality in the U.S. to pass such a measure, a humane society spokeswoman said.