Penicillin is natural antibiotic and have been in use since last century to treat bacterial infections in both humans and animals. Now many bacteria have developed resistant against penicillin and that is why many new antibiotics are being invented. One of the major side effects of penicillin shot is allergic reaction. If you use this drug in dogs then he can have hives, rashes, selling of face, mouth, tongue etc. Oral penicillin can cause diarrhea in dogs.