"It was just a mutual thing where it was best," Jackson said. "The clubhouse [at Fenway Park] is small, a very small place. All the media is there. I didn't want to be a disruption."
A baseball source said the team was concerned about Jackson making matters worse and distracting the current Yankees in front of a heavy media contingent during a weekend that included FOX's nationally televised game on Saturday and ESPN's broadcast on Sunday.
It is not known when Jackson will return to the Yankees' clubhouse.
On Thursday, Jackson released a statement through the club.
"In trying to convey my feelings about a few issues that I am passionate about, I made the mistake of naming some specific players," Jackson said in the statement.
"This was inappropriate and unfair to those players, some of which are very close friends of mine. I think there are ways to speak from the heart without hurting people, and I'm disappointed that I didn't take greater care in expressing my views.
"I have been proactively reaching out to make personal apologies to those within the Hall of Fame community that I offended, and to the Yankees organization for any disruption that I caused in the clubhouse. I continue to have a strong relationship with the club, and look forward to continuing in my role with the team. As always, I remain dedicated to the great game of baseball."
Jackson told SI that he has an issue with players linked to performance-enhancing drugs who have passed his 563 home runs on the all-time list, a group that includes Rodriguez, who has admitted to using steroids with the Rangers from 2001-03.
"Al's a very good friend," Jackson told the magazine. "But I think there are real questions about his numbers. As much as I like him, what he admitted about his usage does cloud some of his records."
Jackson also took aim at the Hall of Fame for inducting what he believes to be unworthy players, a group that included Gary Carter, Kirby Puckett, Phil Niekro, Don Sutton, Jim Rice and Bert Blyleven.
Jackson added that he would not attend the Hall of Fame induction ceremonies for any player believed to have used PEDs, with the possible exception of Andy Pettitte, whom he considers a friend.
Rodriguez said that Jackson reached out to him and explained his comments, though Rodriguez remained tight-lipped on the contents of the conversation. On Friday, Rodriguez offered a wisecrack, making light of his relationship with Jackson.
"With friends like that," Rodriguez said, "who needs enemies?"