A mad first half which saw five goals, two penalties and a red card decided this whirlwind encounter with Boro's 10 men holding out heroically after the break.
The match got off to the most frenetic start as Francois Zoko's header from Luke Freeman's cross was deflected into the net by Elliott Omozusi in the second minute.
Lucas Akins then doubled Boro's lead by nodding in Felipe Morais' centre, only for David Mooney to quickly pull one back for Orient with a well-taken volley.
Then, with still only 16 minutes played, the hosts were awarded a penalty as Omozusi handled Freeman's shot with Jamie Jones just unable to keep out Morais' spot-kick.
Stevenage's Roarie Deacon was then sent off for tugging back Shaun Batt before Lloyd James reduced the deficit again on half-time from the penalty spot after Jayden Stockley was taken late.