Andujar suffered the injury just three games into the season and spent all of April on the injured list. He returned to action on May 4 and made nine appearances before returning to the IL on Monday.
James Wagner of the New York Times reported the expected recovery timetable is four to six months.
Andujar was hitting .128/.143/.128 with no extra-base hits and just one RBI in 49 plate appearances this season. He was just 1-for-27 in his final seven games prior to his second trip to the IL.
"Miguel tried to give as much to the team as he could but realized that he just wasn't physically able to deal with the pain and still be as productive as we all know he can be," Andujar's agent, Ulises Cabrera, said, per Wagner.
According to the New York Post's Dan Martin, Yankees manager Aaron Boone revealed Andujar's recent MRI was "about identical" to the one he underwent following the initial injury.
"The small labrum tear is still there, it hasn't changed at all. The rest of the shoulder is pretty good and stable. I think over the next 24 hours, he's gonna have those conversations with his family and with us to figure out the best course of action: whether to go down the road of surgery or whether to continue to rehab. These will be the decisions made over the next 24 hours."
A platelet-rich plasma (PRP) injection had been ruled out at that point.
Losing Andujar for the remainder of the season is a huge blow to New York's offense. Last year, he finished second in American League Rookie of the Year voting after he hit .297 with 27 home runs, 47 doubles and 92 RBI in 149 games.
That type of production would be hard for any team to replace, but it will be especially tough on the Yankees, who have been bitten by the injury bug early and often this season. Outfielder Aaron Judge, outfielder Giancarlo Stanton, shortstop Didi Gregorius, shortstop Troy Tulowitzki and first baseman Greg Bird are all currently on the injured list.
New York acquired first baseman/designated hitter Kendrys Morales earlier this week to try staying afloat amid all of the injuries.