Could this make my puppies sick?

Rabies would be a way way way outside very-unlikely thing.  Because honestly?   In a tussle with a rabid animal, even one that small, it's not likely a puppy would win.  Rabid animals are crazy -- literally and figuratively.

 However, that being said -- you can call your local fisheries and wildlife and they will do an exam on the carcas (a necropsy) -- they can test for various things.  Likely it would cost you but it would be an option.

 Mostly you will want to talk to the vet.  You will want to have fecals done at the very least on ALL your pups (hooks, whips, etc.).  Parvo and distemper would be the biggest risk to a pup and that's not likely from a squirrel (they aren't zoonotic diseases I don't think). 

However -- you've likely learned a very valuable lesson -- policing a pup when it's outside -- there's no substitute for it.  Because quite apart from diseases, the biggest risk isn't squirrels -- it's other wildlife, snakes, and even human predators (bunchers, etc. looking to steal your dog right out of your yard and gsd's tend to be quite valuable on the black market)

 But now that you know he's extremely prey-driven, you'll have to watch containment because a fully grown GSD is completely capable of leaping even a 6 or 7 foot fence to chase something. 

You may want to re-think feeding wildlife -- because more than just squirrels are drawn to feeders. 

PS -- the other thing to watch for is any sign of bacterial sickness -- simply from rotted meat (since this was days old) -- pups take a while to develop their immune systems. 

Signs?  Things like generally lethargic, sick-acting, avoiding people, upset stomach or not wanting to eat, sticking their head in the corner and avoiding light or human contact. (ANY of those, not just all)

Thanks for the reply. Where I live snakes and dangerous wildlife are virtually non existent. The only venomous snake type here lives on the other side of the state, where it is much more arid. Bobcats, coyotes, fox, etc.... just unheard of in this area (though true, that doesn't mean a one in a million thing couldn't happen.) The only thing I watch for is birds of prey. I regularly put my adult dogs in the yard alone. The puppies do not go outside without supervision. If I run in to grab a drink, the phone, use the restroom, I make sure they are accompanied by at least one adult dog. Lack of supervision for the beagle pups isn't really a problem. I was with them when they grabbed the squirrel, and though I shouldn't have been distracted, they were being guarded. I have poultry netting used at the base of my fence that continues about a foot out onto the ground so digging out isn't an option and a 6 ft privacy fence all around. I will keep your advice in mind that a GSD can scale a fence that height. He is mixed down smaller so I don't know if that is possible for him. He behaves fine with the neighbors cat, my rabbit, etc. I will definitely watch him for signs of increasing prey drive though. Thanks for verbalizing it for me, bacterial sickness is what I'm really worried about. Do you know roughly how long it would take for symptoms to show up? Still waiting on a call from the vet.

Beejou

Thanks for verbalizing it for me, bacterial sickness is what I'm really worried about. 

Basically this is food poisoning, so I would expect any problems to show up within 48 hours.  I had a bad sandwich one evening and I was very ill the next morning.

calliecritturs

You will want to have fecals done at the very least on ALL your pups (hooks, whips, etc.). 

How old are your pups?  Puppies over 4 weeks of age (28 days) weighing more than 2 pounds can take Interceptor which would protect against heartworms, roundworms, hookworms, and whipworms.  A heartworm "preventative" will only kill heartworms less than about 45-days-old (with the age being the time from the infecting mosquito bite).

Pups under 6 months do not need to be tested for heartworms before starting a "preventative" like Interceptor.  That is because it takes 6-7 months after the bite of an infected mosquito for a heartworm infection to show up in testing. 

Dogs/pups that start a "preventative" after the age of 6-weeks should be checked for heartworms 6-7 months later.  This would detect any heartworms that were

• over 45 days old at the time that the "preventative" was started and
• which have developed into adults.

Bacterial infection -- yeah -- it can be 20 minutes later to a day or 2 later.  One of my dogs got mega sick 2 years ago.  We're in Florida (bacteria capital of the known universe??? *sigh*) -- somebuddy puked outside.  Foxy ate supper one night, but the somehow decided he was still hungry ... went outside and ate the vomit (gotta love em *sigh*) -- but this was probably 24 hours after someone regurgitated it (completely undigested and had probably been in the hot Flooor-daaa sun for a whole day - LOVELY!!).

he came in and promptly threw up both what he had 'found' outside AND what he'd eaten half an hour previously.  I heard him in the kitchen and went to check it out and saw the two 'piles' of regurgitated food.  I recognized it as what he'd eaten just previously and also what had been served the night before (I home cook).  When I picked it up one had obviously not been in the stomach long (much cooler than what he'd eaten for 'supper' half hour before that had already reached near body temp and what he'd snagged outside was still quite cool).

Within an hour he was deathly ill.  He'd already emptied his stomach (little piglet -- except this WAS my 'senior' dog who was then 17 1/2) but he was staggering, head into a corner "leave me alone I want to die" attitude.  We raced to the e-vet.

 He was SO sick -- the bacteria dove straight for his liver and literally within hours the liver looked like he was dying of liver failure.  (In fact the vet tried to get me to put him to sleep despite what I KNEW had happened.)

LONG story made short -- I literally demanded they put him on antibiotics (IV) and he made it.  The next morning he went to our own vet .... and eventually they all concurred that it was what I said -- a hellacious bacterial infection (food poisoning?  let's call it MEGA BAD JUDGMENT FOXY!!!!)  Antibiotics for a couple of weeks and some really lengthy coddling of the liver and he pulled thru amazingly well.   He made it to 19! 

Me?  soon after I found a really good colorist to cover the grey ... LOL