The twins, born in December, were fused at the liver and chest.
Swiss media say doctors had originally planned to separate them when they were several months old but brought the operation forward when they each suffered a life-threatening condition.
The operation reportedly carried a 1% chance of success.
The twins, named Lydia and Maya, were born eight weeks premature at the Inselspital hospital in Bern, along with a triplet who was fully separate and healthy.
The hospital said the twins were "extensively conjoined on the liver, but had all vital organs".
They weighed just 2.2kg (4lb 14oz) together. One of the twins had too much blood, and very high blood pressure, while the other one did not have enough.
A 13-strong medical team took five hours to separate the girls on 10 December.
"Such small conjoined siblings had never been successfully separated before," the hospital said.
The head of paediatric surgery, Steffen Berger, paid tribute to the medical staff, saying: "The perfect teamwork of physicians and nursing personnel from various disciplines were the key to success here. We are very happy that the children and parents are faring so well now."
The girls underwent further surgery to close their abdominal walls and are now recovering in a paediatric intensive care ward.
The hospital says the children are "still very small" but developing well.
Le Matin Dimanche newspaper said they had put on weight and begun breastfeeding.
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