Substitute Gavin Tomlin's header in the fifth minute of injury time earned Yeovil their third successive victory.
It won a dour contest of few chances, the best of which came in the first half when Yeovil's Aaron Brown headed against the legs of keeper Jamie Jones.
With time running out, Orient raised their game and had penalty claims waved away when Charlie Daniels was brought down in the box.
And minutes later they were made to pay, as Tomlin snatched the points.
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