The Academy squad travelled to Hemel Hempstead for their final clash of the campaign but were undone by goals from Ryan Howley and Harrison Nee.
The loss put an end to a six-game unbeaten run for Palace, but Paddy McCarthy's side are able to look back with pride on a season that saw huge wins over the likes of Birmingham City, Cardiff City and Watford and many of the lads step up to support the Under-23s' efforts.
Yesterday's game means the Eagles' opponents Coventry end the season sitting ninth with Cardiff pipping Ipswich Town to first-place.
Palace: Luthra, Trialist, Chamberlin-Gayle, Parris, Jude Russell, Trehy, Keutcha, Trialist, Gordon, Aveiro, Ajayi (Gurung 70).
Subs not used: Jacob Russell, Onoabhagbe.