The team said their 30-year-old ace is expected to be OK for spring training next year. He was examined Tuesday by Mets medical director Dr. David Altchek in New York.
"It's not the worst," Santana said on a conference call. "Believe me, I'm going to be ready."
The Mets also announced Tuesday that reliever J.J. Putz had a setback in his recovery from elbow surgery and will miss the rest of the season after an MRI revealed "some new fraying and a slight tear" in his right forearm. He will not need surgery and it is merely a preventative measure, the team said.
Santana said he had the same operation after the 2003 season and came back with a career-high 20 wins and the first of his two Cy Young Awards for the Minnesota Twins.
"I know myself," he said. "I've been through this before. I know exactly what it is."
Mets general manager Omar Minaya said Santana was evaluated around the All-Star break as his stats dipped, adding the injury worsened in recent weeks, especially after his last start. The GM said "nothing major was there" during the previous checkup.
"It's mostly soreness," Minaya said on a conference call. "We all want to see Johan Santana pitching in September. But this is a smart move because we want to see him pitching for the long haul."
The Mets had feared a major setback to Santana, who has four seasons left on his $137.5 million, six-year contract. Instead, he will have arthroscopic surgery.
Santana said that had the Mets been in the middle of a pennant race, rather than lagging well below .500, he would've tried to keep pitching.
"I didn't want to shut it down," he said. That said, "you don't want to go out there and blow it and make it worse."
Santana went 13-9 with a 3.13 ERA in 25 starts in his second year with the Mets. Strong at the start of the season, his numbers had dropped noticeably since June -- he was 7-2 with a 1.77 ERA and averaged nearly 12 strikeouts per nine innings before then but was 6-7 with a 4.02 ERA and averaged 5½ strikeouts after.
Manager Jerry Manuel said Santana complained of elbow soreness after his last outing, and the team decided to shut him down. Santana said his recovery time between starts was mostly affected.
"He felt he could still pitch. He wanted to come on the plane and give it a shot," Manuel said before Tuesday night's game at Florida. "When it gets to the point where he says something, then the red flags went up."
The development with Santana came on the same day that the fourth-place Mets traded reliever Billy Wagner to the Boston Red Sox for two players to be named. Lefty pitcher Pat Misch and first baseman-outfielder Nick Evans were recalled from Triple-A Buffalo.
What began for the Mets as a season with hopes of reaching the World Series has fallen apart, leaving them out of contention and wondering when the next injury will occur.
On Monday, the Mets said Santana would be scratched from his next scheduled start because his elbow was bothering him.
"It was never pain. It was discomfort," Mets pitching coach Dan Warthen said. "If he had ever said pain, then he would have never, ever thrown. We all go through discomfort."
Warthen said the Mets didn't pull Santana after the All-Star break evaluation "because at times it didn't hurt him. It really didn't bother him."
"He was able to pitch a couple different times," he said. "Then the last few, you could see the velocity going down, then you really start to concern yourself. Johan never, ever says anything about his own physical pain. Then he actually finally came clean and said this thing really is bugging me."
Santana had arthroscopic surgery on torn cartilage in his left knee last October, after the season ended. He went 16-7 and led the majors with a 2.53 ERA in his first year with the Mets.
The Mets got Santana in a February 2008 trade with Minnesota.
In other injury news, outfielder Jeff Francoeur returned to the lineup after tearing a ligament in his left thumb over the weekend.
Mets pitcher Oliver Perez, meanwhile, was had his right knee evaluated. Manuel said he didn't think the lefty would make his next scheduled start Friday.
"I'm very doubtful," Manuel said. "I'm tired of being optimistic."