It was virtually one-way traffic after half-time, with Orient pushing for the equaliser. Chances came and went and player-manager Dan Curtis was starting to think it would be one of those days where the ball wouldn't go in.
This changed when with 20 minutes to go James Law and Josh Jacovs opened up the Jewdinese defence down the right for Shafron to tuck home the equaliser.
Orient were in front five minutes later when Sinclair found the top corner with a sizzling volley from fully 35 yards.
Loughton saw the remaining minutes out and defended well to pick up another three points.
Loughton manager Dan Curtis told JC Sport: "I would say that was our best performance of the season. The boys worked so hard for each other and deserved the win. We were solid at the back and could of scored five or six today."