"The surgery went very well," according to a news release issued by Buffalo's Erie County Medical Center. "We are hopeful for and anticipate a speedy recovery and successful outcome."
The release was issued just before noon shortly after the operation was completed by Thom Loree, the hospital's director of head and neck surgery department.
During the operation, doctors said they removed part of Kelly's jawbone where the squamous cell carcinoma was found and caused by "chronic irritation at the gum site." Doctors then reconstructed the affected area.
"Mr. Kelly is recovering comfortably at this time," the hospital said. "He will remain here at the hospital until he feels comfortable to go home."
The 53-year-old Kelly had revealed on Monday that he had been diagnosed with cancer about two weeks earlier.
Calling the prognosis for recovery as being "very good," Kelly said tests showed the cancer was isolated to his jaw and had not spread to other parts of his body.
Kelly said it wouldn't be determined until after the operation as to whether he would require chemotherapy.
"I am extremely confident in my road to recovery," he said. "I plan to tackle this challenge head on, as we Kellys always do."
Kelly's wife, Jill Kelly, posted updates on her Twitter account on Friday. She included a picture of chocolate covered strawberries, which she said were brought to her while waiting for the operation to be completed.
"We love our team and our fans!" Jill Kelly wrote, followed by the term "PrayersForJK," which has become popular on Twitter since Kelly revealed he had cancer.
The Bills also posted a picture of Kelly and notes of support on their Twitter account, one of which read: "No one circles the wagons like the Buffalo Bills."
The diagnosis stems from pain Kelly began experiencing in his jaw in December. He initially thought it was an infection, but grew concerned when antibiotics failed to help.
Tests eventually led to doctors removing a nickel-sized cyst from his gums and nasal cavity during an operation in early March. Follow-up tests revealed the cancer.
It's the latest operation Kelly has required over the past two years. He's also had surgery to correct back, neck and hernia problems.
Kelly spent 11 seasons with the Bills before retiring following the 1996 campaign, and has since made Buffalo his home. Known for his fearless, swashbuckling style, Kelly was the face of Bills teams that made four consecutive Super Bowl appearances in the early 1990s, only to lose them all.
Inducted into the Pro Football Hall of Fame in 2002, Kelly still holds nearly every significant career franchise passing record: 35,467 yards, 237 touchdowns and 26 300-yard games.
Kelly intended to draw upon his faith and family, and the perseverance he's developed in facing other challenges in his life both on and off the field. Kelly's son, Hunter, was born with Krabbe disease, an inherited degenerative disorder of the central and peripheral nervous systems. Given little more than three years to live, Hunter died at the age of 8 in 2005.