Safa and Marwa Bibi underwent three major operations, spending more than 50 hours in theatre.
Their mother, Zainab Bibi, told the BBC she was delighted to be taking them back to the rest of their family.
"The girls are doing very well. Marwa has made good progress and only needs a little support," she said.
"We will keep an eye on Safa and take good care of her. God willing, both will start walking."