My DD is allergic to dogs and cats - although most of that comes from the animal saliva (which in turn ends up on the fur!)
She also has a history of food allergies, so we've dealt with both things in the same way. (she comes up in a rash/welts immediately upon touching the animal, especially if she gets licked... but the long-term effect is a runny nose & hayfever symptoms).
The first point of call for us is making sure that we wash any affected area with soap and water as soon as we notice any contact, and sometimes this is enough to prevent the runny nose from starting. Otherwise, we give the child version of Claratyne which comes in a syrup (or you can get Loratidine from your GP which is the same thing). It's a once-a-day dosage, and we find it tends to knock the worst of the reaction on the head. Not particularly natural, but in my mind I'd prefer something that has a real impact on the immune reaction that occurs (not that natural remedies don't, but often they're not as potent). We've also been using Loratidine since DD was about 7 months, so it's ok for toddlers (under medical advice).
Other than that, all I can suggest is just trying to keep her away from the animals? Our DD now comes to us when/if she gets licked by the cat/dog etc, and knows that she needs to wash her hands or face etc.
Good luck, it's a pain.... and in our experience while the food allergies decrease with time, the animal ones seem to stay the same or get worse!

(but hopefully the toddler gets smarter about interacting with them!)