Cheltenham earned their first away league win of the season, despite being a man down for the last 18 minutes.
Barry Hayles shot the visitors ahead on four minutes but the home side levelled through Adam Boyd's penalty after Drissa Diallo's tackle on Dean Morgan.
On 72 minutes Cheltenham's Ashley Vincent earned a second yellow card but six minutes Ian Westlake's drive restored their advantage.
Orient almost hit back but headers from Adam Chambers and Boyd hit the bar.
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