Hospital sources said the twins were in stable condition as doctors continued working to separate blood vessels and reshape the children's skulls and faces.
"The physical separation of the conjoined twins occurred at 11:17am (16:17 GMT)," a statement from the Children's Medical Centre in Dallas, Texas, said.
Doctors said the lengthy surgery that began on Saturday could last until Monday.
The two-year old twins, Muhammad and Ahmad Ibrahim shared an intricate network of blood vessels, as they were conjoined at the crown of their head.
Born in a small town 800km south of the Egyptian capital, Cairo, the twins have lived in Dallas since June last year, where doctors have been observing them for more than a year.
As the intricate operation progressed without any complications, doctors said the boys' brains had been separated almost completely. But they still shared a complex network of blood vessels which must be divided one by one.
"Our sense is we are probably dealing with 50 to 100 veins," Kenneth Shapiro, one of the five pediatric neurosurgeons said.
"The physical separation of the conjoined twins occurred at 11.17 am(1617 GMT)"
The twins are being operated on on a custom-made bed that spins 360 degrees, and can be split into two once the twins are separated, allowing surgeons to work simultaneously on both.
The operation is very risky, but after studying the twins at length, doctors concluded that the risks were worth taking since the children would have been increasingly inconvenienced had they stayed conjoined.
A similar operation to separate Iranian twins had resulted in the death of both sisters months ago.
The boys' parents are in seclusion and have been receiving hourly updates on the operation.
The twins' medical care has been funded by public donations. If they survive the surgery, they will still need months of therapy to help them recover and learn to function separately.