Dr. James Andrews will perform the procedure later this month.
Harvey had been steadfast in saying he planned to rehab and undergo a throwing program over a six- to eight-week period in order to be able to pitch next season with a partially torn ulnar collateral ligament in his right elbow.
Alderson and other team officials, however, had portrayed that strategy as an uphill battle and regularly had suggested surgery was the likely route.
The GM indicated Friday night that Mets doctor David Altchek and Andrews agreed that Tommy John surgery was the prudent route, although they also were willing to let Harvey try the throwing program to disprove the need for the procedure.
"Based on the conversations that I had with both of the doctors, I felt this would be the right decision," Alderson said. "So in that sense I'm happy Matt has reached the same conclusion."
Harvey reached the surgery decision without ever going to the Mets' complex in Port St. Lucie, Fla., to begin the planned throwing program. He recently had been getting physical therapy at the Hospital for Special Surgery in Manhattan.
"I've become pretty close with Matt, and we've been talking over the last few months, and especially the last week or so. I'll put it this way: If it was me in the same situation, I'd do what he's doing," Mets captain David Wright told ESPNNewYork.com. "The last thing you want is you are a No. 1 starter, you've been as dominant as you've been, and you take the mound every fifth day and in the back of your mind you know that on any given pitch it could go. Your velocity is down that day and all of a sudden you start wondering, 'Is this the day?' Your forearm gets tight and you have those doubts in the back of your head. For me, this is the right decision.
"I know he was fighting -- going back and forth with himself -- trying to figure out what the best situation would be. But I think this is best for us as an organization, and I think it's best for him personally. So it's almost a sense that you're relieved, because the decision has been made. You know exactly when he's going to be pitching again. And you go from there."
Mets officials, gathered for planning meetings this week at the team's Florida complex, expected this result and had been plotting their offseason strategy to pursue starting pitching figuring Harvey would be unavailable.
"I think Matt came to this decision through the course of his rehab prior to commencing throwing in part because, No.1, he had quite a bit of time to think about it," Alderson said. "Perhaps his initial, more emotional response to the injury and his sort of adamant desire to rehab was reconsidered over time. ... After a period of time, he just decided based on all the information that he had that this was a more sort of reasoned approach to the injury.
"As far as we're concerned at the team level, I think we always assumed that at some point Matt would reach this conclusion. ... So this doesn't really change our planning at all, but it does provide some clarity, of course, that we didn't have."
Alderson described the success rate for Tommy John surgery as 85 to 90 percent -- among the more reliable procedures pitchers undergo.
Despite the organization's prevailing belief that Harvey ultimately would commit to surgery, manager Terry Collins said he was a "little surprised" the All-Star would miss next season. Collins based his belief on how adamant Harvey was for weeks about overcoming the ligament tear without surgery.
"This guy has got some kind of demeanor about himself to where he said, 'Listen, I'm going to get through this,'" Collins said. "I have not talked to him, but we all think, obviously, it's going to be the best thing for everybody and this guy is going to come back in 2015. He's going to be, what, 16 months out of surgery? And that's going to be great, because we know he's going to be 100 percent when he walks back out on that mound."
They likely will need to acquire two starting pitchers this offseason -- one who is capable of logging 200 innings and a fifth-starter type to compete with prospects Rafael Montero, Jacob deGrom and Noah Syndergaard. The Mets had veterans Daisuke Matsuzaka and Aaron Harang audition with the club late this season, so re-signing one for the latter role is plausible.
Alderson said he would prefer letting all three prospects open next season in the minors, which would necessitate two external additions. He noted that opening the season with a rookie in the rotation would have a ripple effect of lessening the available reinforcements as the season progresses.
"It's a possibility," Alderson said about breaking camp with a prospect in the rotation. "I don't think it's the kind of scenario that we would prefer. If you look over the last couple of years, we've tended to bring guys up in the middle of the season after pitching more extensively at Triple-A, but we'll just have to see.
"Rafael Montero spent a lot of time in Triple-A last year -- deGrom as well. Syndergaard is probably a little behind them just in terms of his experience at the upper levels. But it's conceivable. The problem with it is that we limit our depth behind the individual."
Added Collins: "I would certainly think we'll probably bring somebody in. Now will it be Dice-K? Will it be Harang? Is it going to be Doc (Roy) Halladay? I have no idea. I can't tell you who it would be, unless you're willing to give one of those kids a chance. And I don't know where that mindset is, either."
Collins believes the prospects could contribute if asked.
"You know what? I'm not afraid of them. I know that," Collins said. "From all that I've heard, I'm not afraid of giving them a shot."
Harvey went 9-5 with a 2.27 ERA in 26 starts this past season, striking out 191 hitters in 178 1/3 innings while allowing 135 hits in his first full season with the team. His WHIP was 0.931.