Richie Wellens side had secured top spot a week earlier with victory over Crewe and, after following that up with a midweek win at Mansfield, hoped to end their home campaign on a high.
But Stockport had not read the script, taking a fifth minute lead through Akil Wright’s header.
Callum Camps doubled the lead with a powerful shot from the edge of the box on nine minutes to leave O’s shellshocked.
And after Tom James and Paul Smyth had seen crosses go begging, Rob Hunt was shown the first yellow card of the game on 20 minutes.
Kieran Sadlier had a shot deflected away for a corner midway through the half, with Jamie McCart edging the ball over the crossbar from another set-piece on 31 minutes.
Smyth was booked for dissent when a free-kick did not go his way, then saw a great ball into the box evade Sadlier.
Stockport’s Myles Hippolyte was booked for pulling back Smyth in stoppage time, with James seeing his free-kick kept out by Ben Hinchcliffe.
And George Moncur had an effort blocked early in the second half after more good work from Smyth, before Richie Wellens made a triple change just before the hour.
Hinchcliffe denied Charlie Kelman, when he looked destined to fire home on 64 minutes, and the same player had an effort deflected wide after a pass from Ruel Sotiriou.
Theo Archibald and Dan Happe returned from injury in a double change on 74 minutes but Stockport added a third soon after through a Connor Lemonhaigh-Evans header.
Kelman and Sotiriou saw late efforts blocked, while Hunt fired over as O’s failed to find a consolation.
But they were able to receive the silverware and celebrate their achievements after the final whistle.
Leyton Orient: Vigouroux, James (Archibald 74), Beckles, McCart (Happe 74), Hunt, Pratley (Brown 58), El Mizouni, Smyth, Moncur (Drinan 59), Sadlier (Kelman 59), Sotiriou.
Unused subs: Sargeant, Clay.
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