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 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.
Rotherham ground out a place in the last four of the Northern Area of the Johnstone's Paint Trophy with a 2-1 win at Hartlepool.
The Millers took the lead after eight minutes, Tom Eaves firmly planting a header home from Kieran Agard's corner for his first goal for the club.
The rest of the half was one-way traffic, but all Pools had to show for their effort was Andy Monkhouse's 24th-minute leveller - the former Miller rolling his finish across keeper Adam Collin.
But, after 44 minutes, the Millers regained the lead. The ball was rolled into the path of Agard and his shot was covered by keeper Scott Flinders, only for a big deflection to wrong-foot the keeper.
Oldham produced a storming fightback to beat Notts County 5-1 and move into the Johnstone's Paint Trophy Northern Area semi-finals.
County struck after 13 minutes when Ronan Murray wriggled free inside the box and slotted home an angled eight-yard shot. Oldham levelled on the half-hour as Korey Smith crossed from the right and James Tarkowski volleyed in from close range.
But the Latics led on the stroke of half-time when Danny Philliskirk blasted in from the penalty spot.
County went down to 10 men in the 55th minute as Dean Leacock was adjudged to have hauled back Jonson Clarke-Harris just outside the box and was sent off for denying a clear goalscoring opportunity.
Oldham cashed in after 67 minutes, with Philliskirk teeing up the unmarked Dayton to score with a low drive from 10 yards. And Philliskirk struck again six minutes from time when he collected Dayton's pass 12 yards out and slammed in his second of the night.
Oldham made it five in injury time as Philliskirk's shot was saved and Clarke-Harris tapped in the rebound.
Ollie Banks scored his first goals for Chesterfield as they deservedly beat Rochdale 3-0 in an entertaining Johnstone's Paint Trophy Northern Area quarter-final at the Proact Stadium.
Banks headed the first and sealed victory with a close-range finish after Armand Gnanduillet had put Chesterfield two up in the 73rd minute.
Britt Assombalonga fired Peterborough to within three matches of Wembley as they edged out Dagenham 1-0 in the Johnstone's Paint Trophy Southern Area quarter-final.
The club's record signing could hardly miss from four yards after being picked out by a 57th minute cut-back from Nathaniel Mendez-Laing as Posh saw off League Two opposition for the second time in four days - this success following hot on the heels of an FA Cup first-round triumph over Exeter.
Nicky Ajose grabbed an injury-time winner as Swindon came from behind to snatch a dramatic 2-1 Johnstone's Paint Trophy victory over Wycombe at the County Ground.
Swindon trailed 1-0 to a late first-half goal by Matt McClure, but Ryan Harley's 25-yard free-kick cannoned off Ajose, completely wrong-footing goalkeeper Matt Ingram and bouncing into the far corner with 14 minutes to play.
With a penalty shoot-out looming, Swindon grabbed their winner.
McEveley's free-kick was headed back at the far post and Ajose spun on the turn to send Mark Cooper's men through.
- Sports & Recreation