The Hall of Fame said in a statement Monday that the board had accepted Alomar’s resignation letter from the board. Alomar submitted the letter on Saturday, the statement said.
Alomar, who was inducted into the Hall of Fame in 2011, will always display his plaque there.
The Blue Jays severed ties with Alomar and Major League Baseball fired him as a special consultant following the investigation’s findings.
MLB commissioner Rob Manfred announced on Friday that Alomar had been fired from his consultant post and placed on the league’s ineligibility list following the results of the independent inquiry.
Manfred said a baseball industry employee reported an incident earlier this year involving Alomar from 2014.
Shortly after the MLB made its decision public, the Blue Jays announced they were cutting ties with Alomar, who was an integral part of back-to-back Toronto World Series titles in 1992 and 1993.
The Blue Jays have said that Alomar’s name will be removed from the Rogers Center level of excellence and that a banner at the Rogers Center commemorating his retired No. 12 and Hall of Fame induction will be removed.
He was also fired as the team’s special assistant.
The allegation was not tested in court, and the lawyer for the woman who reported the incident said her client had no plans to sue Alomar or take further action.
Alomar said he was “disappointed, surprised and upset” by the MLB decision.