Rochdale recorded their first ever win at Brisbane Road when Lee McEvilly drilled home a penalty during first-half stoppage time.
It was Orient's third successive home defeat in front of 2,363 fans - their lowest League gate of the season.
But Orient only had themselves to blame as they created most of the chances in this grim Nationwide Division Three affair.
The turning point came in the 45th minute when O's defender Donny Barnard clumsily hauled down the ever-dangerous Patrick McCourt and referee Frazer Stretton pointed to the spot.
McEvilly duly obliged coolly scoring the penalty.
Orient midfielder John Martin had already missed a hat-trick of chances before Rochdale scored with their first real opening.
First, Martin's jinking run carved open the Rochdale defence but his shot was deflected away for a corner before Chris Tate headed over the bar.
Gary Alexander's shot was then deflected into Martin's path but he wastefully shot straight at keeper Matthew Gilks.
Martin's volley was then superbly saved by Gilks seconds before Rochdale grabbed their shock lead.
In the second half Barnard made way for striker Jabo Ibehre and the O's piled on the pressure without creating too many chances.
Defender Billy Jones crossed for Alexander who just failed to toe-poke the ball home, while Ciaran Toner and Scott Canham went close to levelling.
However, it was Rochdale who missed the easiest chance to stretch their advantage when McEvilly saw his close-range effort scrape the top of the Orient bar.
A delighted Rochdale boss Paul Simpson said after the match: "It took us five hours to get here but we came to do a job and did just that.
"The mood in the camp has changed over the past few days. I had a chat with a few of the players after Saturday's disappointing defeat and it seems to have worked."