The Shih Tzu siblings - thought to only be around 12 weeks old - were found in a black bin liner at the side of a bin in Atherton, the RSPCA said.
One of the puppies had already died.
The other was taken in for emergency veterinary care but died from parvovirus - a highly contagious disease in dogs.
The RSPCA has now launched an investigation to try and find the person who dumped the 'terrified' pups.
Animal welfare officer Steve Wickham said if they had not been found, the puppy that was still alive would have suffered a slow and lingering death.'
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