Rays infielder Akinori Iwamura tags out the Red Sox’ Jacoby Ellsbury on an attempted steal of second base during the sixth inning last night.

AP / Mike Carlson

ST. PETERSBURG, Fla. –– Having learned their lesson from the last time around, the Red Sox and Theo Epstein are nearing a contract extension that will keep the general manager with the team for multiple seasons.

When Epstein’s last deal expired, at the end of the 2005 season, he left the organization briefly before agreeing to return months later.

After the fallout from last time, the two sides have been quietly working to get a new deal done out of the spotlight.

Principal owner John Henry told the Boston Globe yesterday that an agreement had been reached, but later recanted.

“I got a little ahead of where we are today in commenting on what have been refreshingly private negotiations,” Henry wrote in an e-mail. “We are not done, but we expect to have an announcement very soon. I have asked all involved not to comment until this is done.”

Since taking over as GM in 2003, Epstein has seen the Sox win two World Series championships, and they will soon clinch their fifth playoff spot in six seasons.

He’s also overseen a scouting and player-development system that has consistently produced home-grown players through the draft.

“I certainly can’t imagine being here without Theo,” said manager Terry Francona, whom Epstein hired after the 2003 season. “(An extension) should get done –– he’s done a great job.”

It’s a girl

Jason Bay left the team yesterday to return to Boston, just in time to attend to the birth of daughter Evelyn Jane, born last night at 6:47.

The plan had been for Bay’s wife Kristen to have labor induced tomorrow, an off-day, but that plan had to be scrapped when labor began yesterday.

The Sox expect he’ll rejoin the team in Toronto for the start of the weekend series Friday.

In the meantime, the Sox had Jacoby Ellsbury in left field, Coco Crisp in center and Mark Kotsay in right last night with Bay absent.

Bat, ball authenticated

Jason Varitek obtained the bat and ball from his homer on Monday night, the 158th of his career as a catcher, and had both items authenticated. That enabled him to pass Hall of Famer Carlton Fisk for the franchise record at the position.

“I’ve been fortunate to be in the same place for a long time,” said Varitek of the accomplishment.

Best in Sox history

Daisuke Matsuzaka, who won his 17th game Monday night in the series opener, now sports an .895 winning percentage (17–2), the best in Red Sox history for a pitcher with at least 15 decisions, and seventh highest in MLB history.

Matsuzaka’s 32 wins over his first two seasons are the most by a major-league pitcher in his first two years since Houston’s Roy Oswalt won 33 in 2001-02, and the fourth most in club history. Dave “Boo” Ferriss won 46 games in his first two seasons (1945-46).

smcadam@projo.com