Callum Ainley put the Railwaymen in front before they quickly doubled their advantage through Ryan Wintle and on the stroke of half time George Cooper gave the O’s a mountain to climb.
The O’s made one change to the side which won 2-1 against Hartlepool United on Monday with Tom Parkes coming back from suspension to slot into the back four, while Teddy Mezague moved into a central midfield role in the absence of Liam Kelly through injury.
The early chances fell the way of the Railwaymen as a ball in from Cooper was just missed by former O Chris Dagnall in the box.
Opportunities were few and far between in the opening stages, but they came the way of the hosts and George Cooper saw a shot held comfortably by Sam Sargeant, and then Parkes produced a fine last-ditch clearance to deny Dagnall a shot on goal.
Bakayogo then advanced down the left after 22 minutes who played the ball in to the near post but Cooper could only direct the effort wide of Sargeant’s goal.
The hosts finally broke the deadlock though in the 26th minute when a ball into the box found Callum Ainley but his weak sidefooted effort just trickled past Sargeant and the O’s would have to come from behind to maintain our English Football League status.
One soon became two for the hosts as a corner from the right was swung in to the back post and Ryan Wintle’s header was deemed to have crossed the line despite Teddy Mezague’s last-ditch effort to clear.
Dagnall was the next to get a shot away but Sargeant was equal to the fierce effort as the O’s were certainly under the cosh for the majority of the opening period.
The game for the O’s was effectively over though when a long ball forward found the run of Dagnall and he played the ball into the path of Cooper and he rattled an effort past Sargeant to make it 3-0 to the hosts at the half-time break.
Riza made two changes at the break with Paul McCallum and Josh Koroma coming on for Michael Collins and Teddy Mezague as the O’s looked to give themselves a glimmer of hope.
That did little to stem the tide though and Crewe continued to dominate the game in terms of chances as Cooper saw a shot held by Sargeant with just half an hour remaining of the encounter before Dagnall fired straight at the O’s keeper. Wintle then tried his luck from range but the effort was held by Sargeant as the hosts remained on the front foot.
With 80 minutes on the watch the O's had their first real attempt on goal of the afternoon, and Tristan Abrahams fired it well over Ben Garratt's goal, with the keeper being a spectator for large chunks of the game.
Sargeant was forced into another top save up the other end as the game entered the closing stages as he reacted quickly to deny Callum Cooke, before Cooper's fierce effort struck the post.
At least O's got the final shot of the game when Alzate tried his luck from distance, only for Garrett to hold comfortably in the Crewe goal
Two minutes of stoppage time came and went and the O's defeat saw relegation confirmed and it was such a shame that our club's proud history in the Football League came to an end in such fashion.
The O's final home game of the season will see us host Colchester United next Saturday.
CREWE ALEXANDRA: Garratt, Turton, Jones, Dagnall, Cooper (Kirk 90+2), Bakayogo, Bingham, Wintle, Ng, Cooke (Udoh 88), Ainley (Pickering 63).
SUBS: Dawber, Saunders, Udoh, Kiwomya, Finney.
BOOKED: Bakayogo (72)
GOALS: Ainley (26), Wintle (30), Cooper (45+1)
LEYTON ORIENT: Sargeant, Semedo, Parkes, Pollock, Clark, Ochieng, Mezague (McCallum HT), Collins (Koroma HT), Alzate, Adeboyejo (Dalby 74), Abrahams.
SUBS: Janata, Kennedy, Moncur, Dalby, Janse.
REFEREE: M Brown
ATTENDANCE: 3,745 (407 Leyton Orient fans)