Manning decided to have the surgery after consultation with a half-dozen doctors who reached a consensus that the most viable option would be a one-level cervical neck fusion in the wake of his May 23 surgery to repair a bulging disk. It's unclear whether Manning would be able to return to play this season.
The team said in a statement Thursday that the surgery was "uneventful" and that it would not place Manning on season-ending injured reserve and instead keep him on the active roster.
"This procedure is performed regularly throughout the country on persons from all walks of life, including professional football players. Two former Colts players had this same procedure last winter and have fully resumed their careers," the team said in the statement.
"Rehabilitation from such surgery is typically an involved process. Therefore, there will be no estimation of a return date at this time."
The team said that Manning immediately would begin the rehabilitation program prescribed by his surgeon.
The Colts statement came just hours after team owner Jim Irsay wrote on Twitter that Manning would be out "awhile" and coach Jim Caldwell promised to provide more clarity soon. They could have put Manning on injured reserve to open up a roster spot, but that would have meant he would not play at all in a season that will end with in February with the Super Bowl played at Lucas Oil Stadium in downtown Indianapolis.
An anterior fusion procedure usually involves making an incision in the front of the neck, removing soft disk tissue between the vertebrae and fusing the bones together with a graft. The goal is to ease pain or address a disk problem.
Recovery from the procedure typically takes at least eight to 10 weeks, said Dr. Victor Khabie, co-chief of the Orthopedics and Spine Institute at Northern Westchester Hospital in New York. He has not treated Manning, but is familiar with the procedure and how athletes recover from it.
"It could be season-ending, seeing the piggybacking off of another surgery," Khabie said. "But the athletes I've known over the years, I never count out because they are such great competitors and such great healers."
Manning's doctors say his third neck surgery in 19 months went "very well, without complication" and that his prognosis for recovery is good.
Father and son doctors Robert Watkins Sr. and Robert Watkins Jr., who performed Thursday's surgery, issued the statement Friday. The surgery was performed at Marina Del Rey Hospital in California. Manning's previous two surgeries were at Northwestern Memorial in Chicago where Manning had both of his previous surgeries.
The doctors confirmed that Manning needed surgery for a herniated disk and that his rehab program will begin soon.
If Manning recovered in 10 weeks, he would be back around the Nov. 13 game against Jacksonville, the week before the Colts have a bye.
Dr. Andrew Hecht, co-director of spinal surgery at Mount Sinai School of Medicine in New York, doesn't believe the injury will prematurely end Manning's career.
"The odds are that he'll end his career when he wants to end his career," Hecht said.
Manning was unavailable for comment, as was his agent, Tom Condon. His father, Archie, and brother, Cooper, whose college career was ended by a severe neck injury, would not specifically address Peyton's surgical decision.
Archie Manning, a former NFL quarterback, only spoke of his son's state of mind.
"I think he's OK, probably because there's a little finality to this deal in terms of playing," the elder Manning told Mortensen. "He's been on the clock since May. He didn't make it. Obviously, it's a big letdown, but he can relax a little bit compared to the intensity of everything he has done trying to rehab."
Earlier Thursday, without confirming any pending surgery for brother Peyton, Cooper Manning told ESPN that a cervical fusion would be a logical step after his brother's slow recovery and setback last week when he experienced more upper back and neck pain.
"Everyone is different, but I've had a fusion and I've known players who have had fusions and went on to play football. ... You can get a pretty good range of motion back and much more stability once it heals," said Cooper, the oldest of three brothers that include quarterbacks Peyton and Eli.
Cooper said he did not have specific knowledge on a decision regarding another operation for Peyton.
"You know Peyton and how he values his privacy even within a very tight family like we have," he said. "We've exchanged some short texts and I've given him his space. He's had a lot going on."
Manning will miss his first NFL game when the Colts open the 2011 season Sunday against the Houston Texans. He had made 227 consecutive starts counting playoff games, including the Super Bowl the Colts won capping the 2006 season. The four-time MVP is 35 years old.
Manning was hopeful that four months of therapy after his May 23 surgery would allow him to resume normal football activity, but his progress was minimal with nerve regeneration and his triceps area remained weak, not allowing him to throw a football with reasonable velocity. He was taken off the PUP (physically unable to play) list last week so he could practice on a limited basis as a part of his therapy in hopes of making progress and measuring his readiness.
However, Manning's progress "plateaued" and pain returned to his upper back and neck region, which initiated a new set of diagnostic tests and the recent prognosis that an anterior cervical fusion would be a wise course of action, sources said.
On Wednesday, in an interview with ESPN 1050 in New York, Colts vice chairman Bill Polian revealed that Manning would not play the opener Sunday at Houston. Manning confirmed the decision in a statement later Wednesday.
The player who can empathize most with Manning is running back Joseph Addai, who injured a nerve in his left shoulder Oct. 17 against Washington, then missed the next eight games.
There were times, Addai recalled, he would wake up during the night with sudden pain. There were other times he couldn't hold up a microphone or the ball would drop out of his hands with a slight bump.
Addai figured the ensuing bye week would give him enough time to heal, but it took him more than two months to get back into a game and he still didn't feel 100 percent until this season.
"After a while it came back, but you don't really know when it's going to come back," Addai said. "It's frustrating."
Addai said Manning asked him about the experience, something the two discussed at length since players reported to camp July 31.
Addai said he's worried about playing the Texans without Manning.
"You know how important Peyton is," Addai said. "I think everybody has to step it up."
The only other time Manning has missed a regular-season snap because of injury was in 2001 against Miami. Backup Mark Rypien fumbled. The Dolphins recovered and drove 59 yards for the winning score. Manning returned on the next series with a bloody mouth. He was later diagnosed with a hairline fracture in his jaw.
Manning, who rarely misses a snap even at practice, has occasionally been sidelined during the preseason.
He sat out one week of training camp in 1998 before signing his rookie contract. A decade later, he missed all of training camp after having surgery twice to remove an infected bursa sac from his left knee. He also missed some practices after injuring his knee during a preseason game against Minnesota in 2001.
Since being taken with the No. 1 overall pick in 1998, Manning has led the Colts to 11 playoff appearances, 11 double-digit winning seasons, eight division crowns, two AFC titles and a Super Bowl championship.
Chris Mortensen is ESPN's senior NFL analyst. Information from The Associated Press was used in this report.