The goal settled what had been a dour contest between two sides hovering just above the drop zone.
The visitors could have taken the lead when Aaron Brown headed straight at Orient goalkeeper Jamie Jones.
Orient rarely posed a threat although a free-kick from Charlie Daniels was saved by goalkeeper Josh Wagenaar, and a similar effort from Dean Morgan curled just over.
As injury time started, Orient raised their game and had penalty claims waved away when Daniels was upended and Wagenaar punched a cross off the head of substitute Paul Terry.
But it was Yeovil who had the crucial final say seconds later when Tomlin headed home an Andy Welsh corner in the fifth minute of injury time.