Substitute David Graham rose off the bench to light up a scrappy encounter and clinch deserved victory for Torquay.
Graham had been on the pitch only three minutes when he cleverly volleyed the ball past advancing Orient keeper Lee Harrison from Jason Fowler's throughball.
And in the 72nd minute, Graham outpaced Orient defender Matt Joseph in a 40-yard run down the left before toe-poking the ball under Harrison.
Neither side had managed anything like as good until Graham entered the fray.
The match stuttered after a double sending off in only the tenth minute.
Referee Clive Penton dismissed both Torquay skipper Craig Taylor and Orient striker Gary Alexander after a fracas which saw more than a dozen players involved.
Torquay edged the first half, but they still looked lightweight up front until Graham, surprisingly omitted by head coach Leroy Rosenior, supplied fresh inspiration.
Orient's Tom Newey pulled a goal back from David Hunt's free-kick in the 85th minute, but their bad day was completed in the fourth minute of stoppage time.
Left back Matthew Lockwood, visibly frustrated, barged Torquay winger Tony Bedeau in the back as he was holding the ball by the corner flag.
It looked like a booking at worst, but Mr Penton sent Lockwood off.
Rosenior said: "I am delighted and proud for my players. My physio has just told me that we had seven players on the pitch who were injured at the end of the match.
"It would have been very easy for one or two to have given up, but they stuck at it. We always knew that David Graham would come on at some stage, and he gave me just what I wanted." Orient manager Paul Brush said: "The double sending off affected us more than Torquay. But we've lost because two pieces of individual defending weren't good enough."