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09/18/11 6:00 PM ET

Johan throws three innings in simulated game

ATLANTA -- Johan Santana, who was unable to make it back with the Mets this season after shoulder surgery, threw three innings in a simulated game on Sunday in Florida and will next pitch in the Instructional League.

According to Mets general manager Sandy Alderson, the left-hander allowed one hit and struck out four.

Santana made a start for Savannah in the first round of the Class A South Atlantic League playoffs, but he decided not to pitch on Thursday in the championship round against Greensboro.

Santana may pitch in his native Venezuela this winter if he feels up to it and believes it will help him be ready for Spring Training. The Mets remain confident that the two-time American League Cy Young Award winner will be ready to go next season.

Santana was 11-9 with a 2.98 ERA in 29 starts in 2010 prior to September shoulder surgery and has two years and $55 million remaining on the six-year, $137.5 million contract he signed in 2008.

The initial estimates pegged his return to the Mets for June or July this year, but various setbacks stalled his rehab throughout the summer.

Jonathon Niese, on the disabled list since late August with a rib cage injury, will also not make it back this season. The left-hander is 11-11 with a 4.40 ERA.

Mets hope Izzy can return before season's end

ATLANTA -- Jason Isringhausen hasn't pitched since Sept. 6 because of lingering numbness in his right foot, and the veteran reliever, who turned 39 the next day, is starting to run out of time to make it back before the end of the season.

Mets manager Terry Collins, asked when he thought Isringhausen might be available, said, "I'm hoping in St. Louis."

Isringhausen, though, isn't as optimistic.

"I'm hoping for the homestand," he said.

After three games in St. Louis beginning on Tuesday, the Mets conclude the season with six games at Citi Field against the Phillies and Reds. Isringhausen's bounce-back year may have already had an early ending, though.

Given a tryout in Spring Training, Isringhausen was able to stay healthy until the final month and posted his 300th save in San Diego on Aug. 15. Only Mariano Rivera of the Yankees and the Reds' Francisco Cordero have more saves among active pitchers.

But Isringhausen, who has had to overcome numerous arm problems in his career, was sidelined by a herniated disk that is pinching the sciatic nerve and causing numbness in his right foot. He had an epidural last Monday and it was expected that he would need to rest for at least five days.

"He still has some numbness in one of his legs," Collins said. "Doctors say until that's gone, he's not pitching."

Collins, though, says that he still expects Isringhausen, who is 3-3 with seven saves and a 4.05 ERA in 53 games, back before the end of the year. The right-hander, who said he has felt better since taking stronger anti-inflammatory medication in recent days, remains hopeful.

"It had been festering for a while, so I knew it was time to take a few days off," he said.

Byrdak reaches deal to return to Mets in 2012

ATLANTA - The Mets signed left-handed reliever Tim Byrdak to a one-year contract extension on Sunday, general manager Sandy Alderson announced.

Byrdak has appeared in 69 games and is 2-0 with a 2.89 ERA and 46 strikeouts in 37 1/3 innings. He gave up a game-tying RBI single to Freddie Freeman in the seventh inning of the Mets' 7-5 victory on Sunday, but struck out the other two batters he faced to pick up the win.

"We're very happy he's coming back," Alderson said. "It's not typical for us to extend players late in the season like this. But he wanted to come back and we were we happy to do it. He's done a very good job for us."

Byrdak turned out to be a key signing in the winter after Pedro Feliciano signed with the Yankees as a free agent.

Retaining Byrdak gives the Mets two lefties in the bullpen going into next season. Daniel Herrera was recently acquired from the Brewers to complete the Francisco Rodriguez trade.

Left-handed hitters are batting .204 this season against Byrdak, who is making a $900,000 base salary with as much as $300,000 in incentives.

Byrdak, 37, appeared in 64 games with the Astros in 2010 and was 2-2 with a 3.49 ERA.

Reyes pinch-hits, Pagan gets two-day break

ATLANTA -- Jose Reyes said that he wanted to play all three games of the weekend series against the Braves. But after meeting with Terry Collins on Saturday, the shortstop was out of the Mets' lineup for Sunday's finale.

Reyes' left hamstring wasn't acting up. "He's fine," Collins said. But with an off-day on Monday, the manager decided that a two-day break would set the switch-hitter up for the last three series of the year.

"The important part is that he finish this out on a healthy note," said Collins, who revealed that Reyes hopes to play in each of the Mets' nine remaining games.

The Mets begin a three-game series in St. Louis on Tuesday, then close the season at home with three games each against the Phillies and Reds.

Reyes, who was hitless in one pinch-hit at-bat in Sunday's 7-5 win, watched his average drop to .331. He was 0-for-3 with a walk on Saturday in a 1-0 loss to the Braves, falling behind the Brewers' Ryan Braun -- who is at .336 -- in the race for the National League batting title. Reyes has hit in 17 of his 19 starts since coming off the disabled list.

Collins also held center fielder Angel Pagan, bothered by a sore quad, out of the starting lineup on Sunday in anticipation of giving him a two-day break.

"We've got to take advantage of the off-day," Collins said.

Pagan's problem has come over time, according to Collins, who noted that it's been bothering him for a couple of weeks.

Jason Pridie started in center field and replaced Pagan in the two-hole. Ruben Tejada, who moved from second base to shortstop, hit leadoff. Justin Turner, manning second, hit eighth.

Everyone seemed to be looking forward to the Mets' first day off in nearly three weeks.

"There are going to be a lot of guys not getting out of bed for a while tomorrow, I'll tell you that," Collins said.

Class A Savannah falls in championship game

ATLANTA -- The Mets' Class A affiliate in Savannah, which had come within an out of winning the South Atlantic League title the night before, lost to visiting Greensboro, 7-3, on Saturday in the deciding Game 5 of the Championship Series.

Greensboro, a Marlins farm team, rallied with a two-out run in the ninth inning on Friday and won in 11 innings, 12-10, to stay alive. Savannah won the first-half title in the South Division, while Greensboro made the playoffs by winning the second half in the North Division.

Savannah center fielder Darrell Ceciliani batted .394 in the playoffs, but the hitting standout was Greensboro's Marcell Ozuna. He hit .353 with 10 RBIs, three of them coming in the clinching game.

Greensboro took control of Game 5 with five runs (two unearned) in the fourth inning against Savannah starter Angel Cuan. Outfielder Alonzo Harris had a double and a triple for the Sand Gnats.

Savannah was one of three Mets farm teams to make the postseason. St. Lucie reached the Championship Series in the Class A Advanced Florida State League, losing to Daytona. Brooklyn fell to eventual champion Staten Island in the first round of the Class A short-season New York-Penn League playoffs.

Guy Curtright is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.