In a statement on the club's official website, www.mcfc.co.uk Bernstein says: "It is with regret that I have today tendered my resignation as chairman of Manchester City PLC," said Bernstein.
"Over the last few months there has been a divergence of views on fundamental strategic issues, particularly concerning finance and management.
"I believe this has inhibited my ability to direct the club in the way I would wish.
"I have supported Manchester City since I was a boy and I am desperate for us to succeed," he added.
I would like to thank our wonderful fans for their backing. They have been fantastic in their support, which has never wavered even during the most difficult times. I have been touched by their kindness and enthusiasm.
"I wish the club well and hope that it will build on the solid foundations that have been laid."
This shock news follows last week's resignation by City director Chris Bird.