He may be whining just because he feels awful; but, if he continues, I would call the vet and ask what he thinks. That really is great you got him in to see your vet and that he is available today!!
I have a couple of pups I have to just put pills down their throats. They simply will not take them with treats.
Here is a great video that shows how to give meds to a pup:
How To Give Your Dog a Pill Video | Dog Care & Grooming | Howcast.com
Here is another one with a chi....this one is interesting as it suggests giving water in a syringe after. I had never thought of that!