Hello,
The yogurt should be okay as long as you don't give more than a couple tablespoons per day. The yogurt helps add beneficial bacteria back into the intestinal tract.
You could also use a lactobaccillus/probiotic product such as
Culturelle instead of the yogurt.
Having his stool checked for parasites is a good idea, as Labman suggested.
Depending on how old the puppy is, it probably needs it's shots anyway (those usually begin at 7 to 8 weeks of age), so I recommend making the trip to your vet anyway. You can have the puppy vaccinated and tell the vet of your concerns all in one trip.
Good luck!