Carl Baker and Franck Moussa both scored memorable goals before Leon Clarke made sure of victory in the last 15 minutes.
John Fleck, who was pulling the strings in midfield, fed Baker in the 10th minute and the skipper powered a left-foot shot past Jamie Jones who was at full stretch.
Baker sent another shot over the bar while leading score Callum Wilson saw an effort pushed aside by Jones.
Orient survived until the break and looked to have earned their way back into the game in the 57th minute when Jordan Clarke fouled Shaun Batt in the area and the referee awarded penalty.
David Mooney struck the spot-kick low and well but Joe Murphy read his intentions and saved low down to his right.
Nine minutes later Moussa netted with a delightful chip over Jones before Clarke headed home in the 76th minute from a Baker free-kick.
Sub Yohann Lasiment pulled back a consolation two minutes into injury time.