“The collective conduct of the Astros’ organization in 2017 was unacceptable,” he added, “and I respect and accept the commissioner’s discipline for my past actions.”

M.L.B. said that it had reviewed thousands of emails, text messages, photographs and video clips and interviewed 65 people — including 34 current and former Red Sox players — in the investigation, which was prompted by a report in The Athletic on Jan. 7. The Athletic also broke the news of the Astros’ more elaborate scheme in their championship season of 2017, including an on-the-record account from the former Houston pitcher Mike Fiers. The Athletic article on the Red Sox did not cite a player by name, and neither did Manfred’s report.

Manfred said that the players had been granted immunity in exchange for cooperating with the investigation, but also that “this is not a case in which I would have otherwise considered imposing discipline on players.”

He said that Watkins had decoded signs by reviewing video of prior games and conveying that information in scouting meetings before games. A runner from second base could then communicate those signs to the hitter via body movements. All of that is legal and widely accepted throughout baseball, but Watkins was found to have sometimes updated players during games based on signs he had decoded while watching live video, which is prohibited.

Watkins was said to have “vehemently denied” the accusations, but some players said they suspected him of doing it. Manfred said there was no indication that the activity took place during the 2018 postseason, when opponents’ sequences were too difficult to decode.