Goals from Paul Lewis, Kaiyne Woolery and Kieron Morris condemned Embleton to his final defeat in charge of the O’s, with Jamie Turley netting a consolation moments after coming on.
But with just four wins from their last 15 matches, Orient chairman Nigel Travis felt he was left with no choice but to part company with his manager.
“This was an extremely difficult decision for us to make, and one which we have done with heavy hearts,” he said.
“Nobody can underestimate, nor should ever forget, the influence and impact Ross has had on the rebirth of our club.
“He was an integral part of our National League success and he stood up to lead the team following the tragic loss of Justin Edinburgh, and again put himself forward when we were later in need of a head coach.
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