Robert Earnshaw notched his 31st goal of the season to end Cardiff's scoring drought but his side will still have to travel to Bristol City for a tricky semi-final second leg.
The Welsh outfit saved a point at already promoted Crewe when Earnshaw broke the club goalscoring record with a finely executed strike in the 64th minute. But wins for play-off rivals QPR and Bristol City and Oldham's point at Huddersfield push Cardiff back into sixth spot.
It was a terribly disappointing finale for Lennie Lawrence's expensively assembled team as they were pushing Crewe all the way for the second automatic spot until consecutive defeats at the hands of Peterborough, Colchester and Bristol City scuppered their hopes.
They were forced to look on at the rapturous scenes at the final whistle as Crewe picked up their runners-up medals and long serving manager Dario Gradi received a shield which has been introduced this year to runners up in all Nationwide League divisions.
Crewe had nothing to play for but pride and with Lawrence resting players with his eyes already on the play-offs it was no surprise that it was a tame affair.
A rare goal from young defender Richard Walker put the home side in front a minute before half time. Alex leading scorer Rob Hulse had mis-hit a golden opportunity when he was played through on goal, visiting keeper Neil Alexander got a finger to the ball to push it round the post.
And from Kenny Lunt's flag kick Alexander was beaten at the near post as Walker's downward header found the net.
Wales Under-21 international David Vaughan forced a brilliant save from Alexander moments later after a mazy run but Hulse blazed the rebound well wide.
Former Middlesbrough man Andy Campbell shot wide from just eight yards out as Cardiff began to take control in the second half, with the introduction of Graham Kavanagh in midfield and Earnshaw up front being pivotal.
Eventually Peter Thorne laid a neat ball off to Earnshaw who ghosted in on the left-hand side of the box and the Zambian born Welsh international took a deft touch past home keeper Clayton Ince for a deserved equaliser.