Goals by leading scorer Adam Boyd and substitute Jabo Ibehre in the closing nine minutes broke a stalemate to give Orient their first win in eight games.
Home striker Wayne Gray converted a 12th-minute penalty after he had been brought down by keeper Steve Phillips.
Rovers equalised when Rickie Lambert headed home a Stuart Campbell cross.
Both teams squandered further chances before Boyd restored Orient's lead with his 14th goal of the season and Ibehre then scrambled home a third.
Leyton Orient: Morris, Purches, Saah, Oji (Thornton 65), Palmer, Melligan (Barcham 65), Terry, Chambers, Demetriou, Boyd, Wayne Gray (Ibehre 46).
Subs Not Used: Daniels, Shields.
Goals: Wayne Gray 12 pen, Boyd 81, Ibehre 90.
Bristol Rovers: Phillips, Lescott, Elliott, Anthony, Jacobson, Pipe (Williams 84), Lines, Campbell, Disley (Klein-Davies 84), Rigg, Lambert.
Subs Not Used: Hinton, Haldane, Clough.
Booked: Phillips.
Goals: Lambert 29.
Att: 5,132
Ref: Rob Shoebridge (Derbyshire).
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