"He's doing great," a source close to Brady said Thursday in a text message.
Doctors familiar with that type of surgery, but who didn't perform the procedure on Brady, estimate the quarterback will initially be in a walking boot for about six weeks. Their expectation was that Brady should be ready by the start of training camp, if not sooner.
The surgery's completion was first reported by Comcast SportsNet New England.
Brady had a screw inserted in the navicular bone in an attempt to prevent the stress fracture in his foot from becoming a full fracture, and he should be healthy by training camp, a source told CSNNE.com.
The quarterback might even be able to participate in minicamps and passing camps in the spring, according to the report.
Brady played much of this season with the stress fracture, but it did not affect his performance in the Patriots' loss to the New York Jets on Sunday, according to multiple media reports.
Brady was a full participant in three practices leading up to the Jets game.
On Nov. 10, Brady missed his first practice of the season. He was listed that day with a foot injury for the first time on the team's injury report. From that point on, it was common for Brady to be held out of Wednesday practices, while he was limited in practices the remainder of the week.
Brady was listed on the Patriots' injury report with a foot injury for the last eight regular-season games and their playoff game but played in all of them.
A league source told The Boston Globe on Wednesday that the injury wouldn't keep Brady from playing in the Pro Bowl on Jan. 30 in Hawaii, but the NFL on Thursday officially acknowledged that Brady has pulled out of the game and will be replaced by Kansas City Chiefs quarterback Matt Cassel.
Information from ESPNBoston.com's Mike Reiss and The Associated Press contributed to this report.