The team learned that a Sox-rooting construction worker had buried a shirt in the stadium from a report in the New York Post on Friday, team officials said.
Yankees President Randy Levine said the team at first considered leaving the shirt.
"The first thought was, you know, it's never a good thing to be buried in cement when you're in New York," Levine said. "But then we decided, 'Why reward somebody who had really bad motives and was trying to do a really bad thing?"'
The worker had buried a Boston jersey under a locker room in the new stadium, which will open next year across the street from the current ballpark, team officials said.
Levine said that area had been well supervised. "Obviously it was in a different location," he said.
On Saturday, construction workers who remembered the employee - Gino Castignoli - phoned in tips about the shirt's location.
"We had anonymous people come tell us where it was and we were able to find it," said Frank Gramarossa, a project executive with Turner Construction, the general contractor on the site.
It took about five hours of drilling Saturday to locate the shirt under 2 feet of concrete, he said.
On Sunday, Levine and Yankees Chief Operating Officer Lonn Trost watched as Gramarossa and foreman Rich Corrado finished the job and pulled the shirt from the rubble.
Now in shreds from the jackhammers, the shirt still bore "Red Sox" on the front. It was a David Ortiz jersey, No. 34.
Trost said the Yankees had discussed possible criminal charges against Castignoli with the district attorney's office. "We will take appropriate action since fortunately we do know the name of the individual," he said.
A woman who answered the phone at Castignoli's home in the Bronx said he was not there.
A spokesman for Bronx District Attorney Robert Johnson did not immediately return a telephone message Sunday.
Levine said the shirt would be cleaned up and sent to the Jimmy Fund, a charity affiliated with Boston's Dana-Farber Cancer Institute.
"Hopefully the Jimmy Fund will auction it off and we'll take the act that was a very, very bad act and turn it into something beautiful," Levine said.