Yes, by all means give him a dollop of plain yogurt in his kibble every day. It won't hurt him and it will help to repopulate his gut with beneficial bacteria. Particularly keep doing it after he is done with his antibiotics, which will probably kill off the bacteria in the yogurt too. You may even want to find doggie probiotics and use them for a time.
Keep in mind that many yeast infections are caused by diet - too starchy, something the dog is allergic to (allergies cause itchy ears, scratching and irritated skin opens up pathways for infections) - and your dog might benefit even more from a change in diet, depending on what you are feeding him. Usually recommended are diets low in grains and starches, particularly corn, and high in animal proteins.
Also there can be a connection with internal parasites. Whip worm, in particular, is very damaging to the gut and can cause leaky gut syndrome, which really affects nutrition and allergies. Allergies because holes in the gut from the parasite allow larger particles of food to enter into the blood stream, which then trigger allergic responses, which give you the irritated itchy skin and allows the infections.
Komondors also have floppy ears and heavy coats, which can block air flow into the ear canal, giving a perfect place for yeast infections. You can either trim the hair under and on the ear to open up some air flow, or have your Komondor wear a snood at least part of the time to pull the ears back and allow the insides to dry out.
Once the ears are healed up, you can use distilled vinegar to wash them out and even put a dollop of plain yogurt (warmed) into the ears themselves. One of my friends did this with a German Shepherd that came to her with body odor and yeastiness and it entirely cleared her up. I babysat my parent's English Setter years ago, they live in the "wet" side of our state, the land of mold and mildew. He had chronic ear problems and came to me with ear meds... however, in our semi desert area, his ears were clear in a week from the low humidity and lack of mold/mildew in our house. I can't visit their house for more than 3 - 4 days and my allergies are killing me and my ears itch like mad!
Hopefully this will help you with some ideas as to cause that can be dealt with to get him healed up and to stay that way.