Lewis Reilly's first-half penalty to give Crewe the lead wasn't enough as Cardiff City struck an equaliser before half-time and then completed the victory in the second period.
Alex Morris was forced to take a younger than usual group to South Wales on Friday, with a number of his usual squad being kept behind for the first team squad that went to Vale Park the following day.
Crewe: Jaaskelainen, Woodcock, Offord, Lundstram, Sass-Davies, Harrison, Reilly, Griffiths (Johnson), Udoh, Finney, Dale