I hope by now, you have gotten the pup to the Vet! There is no way we can advise you what to do. The injury may be minor or more extensive and a Vet needs to evaluate this.
It is not a good idea to leave a small pup unattended with a larger dog. The pup should be in a safe and secure area if you are not there to supervise it.
Hope the pup will be ok!