When my pets, recently my kitty, have little to no desire for food e.g. prescribed food, we will try a highly favored broth (from chicken soup or the oil from tuna.

Injectable Vitamin B by your veterinarian (and they can show you how to give it) is a safe and often effective appetite stimulant. 

Wysong makes a supplement that often tempts animals to eat that is really a total food source with many vitamins and probiotics – PDG (Pre-Di-Gest) powder. 

If you have a holistic pet store within driving range, visit them for healthy treats and vitamins.

If you need to order on-line, try the Canine Plus by VetriScience (my site has the link). 

The best way to get dogs to eat is to feed them real food.  You can try almost any people food, especially proteins like chicken, fish, beef, eggs, cottage cheese. Vegetables, cooked or raw, are good. For nutrition they need to be pureed in the blender, but as a treat they can be any size. right now do not worry about balance, just getting her started eating again. Begin to read articles (my site, Dr. Becker at Mercola, breeders who have fed raw for generations, Dr. hofve for a few) about feeding a fresh food diet (just as we eat a variety of fresh food, hopefully sustainably or organically raised) to improve health in general. 

Since you did not tell us what type of autoimmune your pup has, there may be blisters in the mouth that are preventing eating, so then the above suggestions would be different. 

Second, I
strongly recommend finding an integrative veterinarian with whom to work. This
is a person trained in many different approaches, including using conventional
drugs only when absolutely needed. Working with one can increase the chance
that your cherished companion can live a long and healthy life after recovering
from this current problem (with holistic approaches most auto immune diseases can be completely resolved, but if not, there are dozens of ways to help her stay happy and fairly healthy). There are good ones and great ones, and a few
homeopathic veterinarians will consult by phone or email. You can go to the web
sites for each type of holistic practice and use their referral list to find
one near to you. Many practitioners are members of only one or two of the
organizations, so you do need to go to every site to find who is near you:

1. Wide range of other treatments: http://www.AHVMA.org, American Holistic Veterinary
Medical Association and http://www.civtedu.org.   
2. Homeopathic veterinarians (these can often help you by phone if no other
holistic practitioners are nearby that you like): http://www.theAVH.org and http://www.DrPitcairn.com.

3. Chiropractic and Osteopathic – http://www.animalchiropractic.org;
http://equineosteopathy.org/ (they
treat dogs, too)
4. TCVM (Acupuncture and Chinese medicine): http://www.IVAS.org,
http://www.aava.org & http://www.TCVM.com

5. Herbal
– http://www.VBMA.org

Since you do not list your state, I cannot be more specific, but you can look at the links page on my site or email me for help. My article on selecting and working with a holistic veterinarian will help you choose one.