The Dons' second string went down to their Motherwell counterparts at Bathgate despite taking a second half lead through Dutch midfielder Jeffrey de Visscher.
Following a goalless opening period, Aberdeen took the lead in the 58th minute when first Tommy Wright and then Mitchel Megginson saw close range efforts blocked before de Visscher scored from close range.
Six minutes later, Well were level when Jamie Murphy headed home a free kick and on 78 minutes Murphy turned provider, his cross from the right being turned home by Mark Smith. Two minutes from time, the home side made sure of the points when Shaun Hutchinson headed home a corner.