NEW YORK -- It's been all but certain for weeks, and now Johan Santana's season has officially ended.

Citing a hesitancy to meddle with Class A Savannah's championship series, Santana declared himself a healthy scratch from Thursday's Game 3 of the South Atlantic League's best-of-five title series. Rather than make a second rehab start for Savannah, Santana will throw a simulated game on Sunday before advancing to instructional league in Port St. Lucie, Fla.

"He doesn't ... want to interrupt what's going on in Savannah," manager Terry Collins said. "He doesn't know how ready he's going to be, and it could be the championship game, and he doesn't feel like that's his place."

If he feels up to it and believes it is necessary, Santana may pitch in Winter Ball in his native Venezuela following the stint in the instructional league. Whatever small chance he had to return to the Mets this season, however, has vanished.

"We were realistic enough to know that this was a day-by-day situation," Collins said, looking back on Santana's lost season. "There was nothing the doctors could promise us, ever."

Though initial estimates pegged Santana's return to the big leagues for June or July, various setbacks stalled his rehab throughout the summer. But the Mets remain confident that the two-time Cy Young Award winner will be fully healthy come Spring Training.

Santana, who was 11-9 with a 2.98 ERA in 29 starts last season prior to September surgery on his left shoulder, has two years and $55 million guaranteed on the six-year, $137.5 million contract he signed in 2008.

Reyes to rein it in on the basepaths

NEW YORK -- Jose Reyes is not completely healthy -- he admits it, and his manager admits it -- and it will alter the way he is used and how he performs throughout the rest of the season.

Reyes will sit out Thursday's series finale against the Nationals, for example, because it is a day game after a night game. And when he does play, he will continue to be somewhat hesitant on the basepaths.

"The only difference that I feel is that when I get on base, I won't be stealing too many bases," said Reyes, who has been receiving daily massages and heat treatments and wearing protective sleeves on both legs. "When I feel better, I'm going to try to steal bases. But right now I'm backing off a little bit."

Though Reyes says that he felt 100 percent when the Mets activated him from the disabled list late last month, the health of his legs has since deteriorated to the point where it is affecting his abilities.

Though Reyes can still help the Mets in the field and at the plate -- his league-leading .333 average is testament to that -- he is no longer an active threat on the basepaths.

But that's not particularly troubling to the Mets, who are more concerned with Reyes' long-term health. There is a fair chance that the team will re-sign its star shortstop following this season, making the health of his legs a significant issue to all parties involved.

"He says he feels fine, and I believe him," manager Terry Collins said. "I just think he's trying to be a little cautious, and a little more aware that he's got to be careful."

Mets announce Sterling Award winners

NEW YORK -- The Mets have been building a large part of their future around pitching, so it was no surprise that pitchers dominated the organization's annual Minor League awards, announced on Wednesday.

Among the Sterling Award winners were top pitching prospects Jeurys Familia and Matt Harvey, who won Player of the Year honors for Double-A Binghamton and Class A St. Lucie, respectively. Harvey (third) and Familia (seventh) both cracked MLB.com's Top 10 list of Mets prospects this summer.

"It was a lot of fun," Harvey said. "It was a good learning experience. I had some ups and downs, but overall I felt like it was a successful season."

In his first full year as a professional, Harvey compiled a 13-5 record and 3.32 ERA over two levels of the Minors, finishing with a 5-0 run and 2.92 ERA over his final seven starts at Double-A.

Equally impressive was the work of Familia, who struck out 96 batters in 87 2/3 innings at Binghamton. Though general manager Sandy Alderson has hinted that the right-hander's future may be in the bullpen, Familia said on Wednesday that he would prefer to remain a starter.

"I feel better when I start the game," Familia said. "I'm more confident."

Other Sterling Award winners included Organizational Player of the Year Josh Satin and Pitcher of the Year Darin Gorski.

The Mets also presented Player of the Year awards at each Minor League level to right-hander Chris Schwinden (Triple-A Buffalo), left-hander Angel Cuan (Class A Savannah), infielder Daniel Muno (Class A Brooklyn), catcher Cam Maron (Rookie League Class A Kingsport), right-hander Rafael Montero (Rookie League Class A Gulf Coast Mets), outfielder Maiki De La Cruz (Dominican Summer League 1) and right-hander Persio Reyes (Dominican Summer League 2).