Mike Diehm of the Lancaster County SPCA said the pups - one male, one female - were nearly frozen when a man heard them crying from inside the backpack Wednesday morning as he walked by. They are believed to be Chihuahua mixes and around two months old.
They have been warmed and are doing well. The shelter staff has dubbed the female dog Breeze and the male Lucky.
SPCA officials said the pups won't be available for adoption until the police investigation into their abandonment is complete.
Anyone with information about the case is asked to contact the Lancaster County SPCA.