Doctors removed that piece of her skull to relieve swelling in her brain. Giffords has been wearing a helmet adorned with an Arizona state flag.
Surgeons will replace it with a plastic implant. They say Giffords should recover in a day or two.
It's another encouraging step since the Arizona congresswoman was shot in the head more than four months ago. The shooting rampage left six other people dead in Tucson on Jan. 8.
The surgery comes two days after Giffords was in Florida to watch her astronaut husband, Mark Kelly, launch into space aboard the Endeavour.
Her doctors have said she has made remarkable progress in what will be a long recovery.
The next step will be to release her from the hospital. Then she will continue speech, occupational and physical therapy at an outpatient clinic.
The Associated Press contributed to this report.