Boro raced into a two-goal lead as Francois Zoko and Lucas Akins found the net with headers. David Mooney quickly pulled one back for Orient with a well-taken volley, only for Felipe Morais to restore Stevenage's advantage from the penalty spot in the 16th minute.
Boro striker Roarie Deacon saw red before Lloyd James' spot-kick on the stroke of half-time gave the League One leaders hope. However, 10-man Stevenage saw out the whole of the second half to progress.
"I was very disappointed about the goals we conceded. It was just three crosses leading to three successes for them and that gave us a mountain to climb," Slade said.
"We managed to get a goal back in between that but we've left ourselves a real mountain to climb.
"I had to re-organise the defence because I wasn't happy and with what I had, I had to try to alter it to see if I could make things any better.
"I shoved Elliot (Omozusi) into the centre and Gary Sawyer back into his familiar left -back but it was just one of those things.
"We managed to nick one back before half-time, which gave us a real lift, and with them down to 10 men it was one-way traffic in the second half.
"I don't feel the referee had a good game - I think there were mistakes there but then again my players make mistakes as well."
- Sports & Recreation
- David Mooney
- Lucas Akins