Heading into Saturday's fixtures, Richie Wellens's League One-bound crop knew that a win over Crewe coupled with Stevenage failing to beat Mansfield Town would guarantee a first-placed finish in the fourth tier.
Orient - whose promotion to League One was confirmed in unorthodox circumstances on Tuesday - would fail to break down the Crewe backline in a goalless first half, but a George Moncur penalty in the 51st minute propelled Wellens's men ever closer to glory.
A 77th-minute Charlie Kelman effort sealed the deal for Orient, who are now guaranteed to be returning to the third tier of English football as League Two champions, as Stevenage fell to a 1-0 loss at Mansfield courtesy of KD Davis's 11th-minute goal.
Wellens's men boast 87 points from their 43 contests this season - seven more than Northampton Town, who have played a game more - while Stevenage can only hit the 85-point mark in their remaining trio of fixtures.
Fans spilled out onto the Matchroom Stadium pitch at the full-time whistle, as the O's returned to League One after an eight-year absence, having been relegated in the 2014-15 season and also spending two years in the doldrums of the National League between 2017 and 2019.
At the other end of the table, though, there was heartbreak for Rochdale, whose remarkable 102-year stint in the EFL came to an end with a 1-0 loss to Stockport.
The Dale - who sacked manager Jim Bentley last month - would be demoted with anything fewer than three points on Saturday, and even a win would not have been enough if Crawley Town overcame Hartlepool United.
Crawley ultimately ran out 2-0 winners in their crucial survival battle, but Rochdale went down with a whimper as Tanto Olaofe scored the only goal of the game in the eighth minute of first-half injury time.
Jimmy McNulty's side have lost 26 of their 44 fixtures this season to glean just 34 points, 11 adrift of 22nd-placed Crawley with just two games left to play this term.
The Dale are now only fighting to avoid finishing dead last in the division, with Hartlepool - whose fate could be sealed next weekend - five points better off than their already-relegated counterparts in 23rd place.