It was first Isthmian Premier setback for Steve King and his side after they began the season with two wins and a draw.
A late Tyano Wilson goal was all they had to show for their efforts and the points went to Wanderers, who had scored through Ade Yusuff and Alex Hernandez.
The defeat leaves the Sports seventh in the table ahead of a bank holiday weekend double, which sees them host Leatherhead on Saturday and visit Lewes on Monday.
See pictures by Lydia and Nick Redman from Cray Wanderers 2 Eastbourne Borough 1 on this page and the ones linked – and get the latest from the Priory Lane camp in the Eastbourne Herald every Friday.
17. Lydia Redman
Cray Wanderers v Eastbourne Borough, Isthmian Premier Photo: Lydia Redman : Lydia and Nick Redman
18. Lydia Redman
Cray Wanderers v Eastbourne Borough, Isthmian Premier Photo: Lydia Redman : Lydia and Nick Redman
19. Lydia Redman
Cray Wanderers v Eastbourne Borough, Isthmian Premier Photo: Lydia Redman : Lydia and Nick Redman
20. Lydia Redman
Cray Wanderers v Eastbourne Borough, Isthmian Premier Photo: Lydia Redman : Lydia and Nick Redman