An MRI taken Tuesday at the Hospital for Special Surgery in Manhattan revealed Santana has lower back inflammation. The 33-year-old left-hander will be placed on the 15-day disabled list retroactive to Aug. 18 but is expected to be shut down for the rest of the year.
Surgery will not be required, Alderson said. Doctors have prescribed rest and medication and intermittent exercise.
"I'm very confident he'll be back next season ready to go, hopefully in a stronger position coming into this season," Alderson said. "If you look back at this season and what we reasonably could've expected at the beginning of the year, he's accomplished quite a lot."
Santana said he began experiencing tightness in his back a couple weeks ago, but it wasn't until his last start Aug. 17 in Washington that he really felt it. He brought up the issue with the organization following a Monday bullpen session.
"My mindset was to start tomorrow, but the doctors are thinking different now, so we'll go with everything they're saying," said Santana, who is due $31 million next year, including the buyout for the following season. "I want to keep pitching. I felt that I could pitch, but at the same time, I'm listening to them."
Alderson is relieved Santana won't need surgery.
"I don't believe it's a disk; it's inflammation in the area of [vertebra] L5," Alderson said, adding there's no concern with Santana's shoulder or ankle. "That inflammation has led to some soreness, but again, I think the important thing is, that the doctors have not recommended surgery."
Right-hander Collin McHugh was promoted from the minors and will start in Santana's place on Thursday afternoon against Colorado. McHugh, 25, went 2-4 with a 3.39 ERA in 12 starts for Triple-A Buffalo.
Since throwing a career-high 134-pitch no-hitter -- the first one in franchise history -- on June 1, Santana is 3-7 with an 8.27 ERA in 10 starts. He has allowed at least six runs in each of his last five outings (0-5, 15.63 ERA).
"I don't have any second thoughts about the way it was handled," Alderson said of leaving Santana in the no-hitter instead of pulling him. "Obviously, it's something that comes up. I think the reason I don't spend a lot of time thinking about it is there's nothing I can do about it. And No. 2, however, is that this is a back issue that was preceded by an ankle issue. Neither of which pre-existed at the time of the no-hitter. This has not been a shoulder issue, so from that standpoint I just don't see a direct correlation.
"As good an explanation as any is that this is a substantial number of innings that he pitched over the course of the season following a season of no activity other than rehab," Alderson continued. "This may just be a way that his body is telling him that it's been a long time since the injury, through the rehabilitation and the number of innings he's pitched this year, and the body is starting to complain. But again, I think it would be very hard to trace it back to the no-hitter."
Manager Terry Collins struggled with his decision to leave Santana in the game.
"No. Not at all," Santana replied when asked if the no-hitter resulted in him being injured now. "That's a long time ago, and this happened just a couple days ago. It's tough to go back and look at that no-hitter and blame it for this.
"Think about my ankle when they stepped on it and the other things I have to do and not being 100 percent and battling through it, you start compensating. But, when I was in that situation in my games, I didn't think about it. I just wanted to compete."
Santana, who missed all of last season after undergoing shoulder surgery, is 6-9 with a 4.85 ERA in 21 starts (117 innings) for the Mets in 2012. He was placed on the 15-day DL in late July with a sprained right ankle.
Collins said at the beginning of spring training the Mets hoped to get 28 starts out of Santana.
Like Alderson, Santana believes he will be ready for the start of the 2013 season, and hopes to work on regaining command of all his pitches.
Alderson also announced that outfielder Kirk Nieuwenhuis, currently with Triple-A Buffalo, was seen by doctors in New York after reporting to Florida to rehabilitate his partially torn plantar fascia. He has been prescribed to rest for a period of weeks, and the Mets GM doesn't expect him back this season.