He had been in the hot seat at Easter Road for three years, and it is thought differences with the other board members prompted his decision.
McPherson said: "There has been no big fall out, but is is important at this time of challenge and change that the team acts and thinks as one. Therefore, I have decided that it is right for everyone that I withdraw. I will continue to support the club in any way that I can."
Malcolm tendered his resignation on Monday, but the shock news was held back until the CIS Cup tie with Alloa was resolved.
New chairman Ken Lewandowski paid tribute to his predecessor saying: "Malcolm has put in tremendous service during his time as chairman and he has an open invitation to the boardroom and we all look forward to seeing him on a very regular basis at Easter Road"
It will be interesting to see what new chairman Lewandowski changes at ER. He is not really known to the majority of the fans, and in my view has to change that. I wish Mr McPherson my best wishes for the future, and Mr Lewandowski my very best wishes for the club.