The incident occurred hours before Palace secured a vital 1-0 win that lifted them out of the relegation zone.
Palace, who still used the vehicle despite the damage, confirmed on Sunday that the team's coach was vandalised and that police had been notified.
"The team bus was covered in graffiti with the words 'Crystal Palace' overnight on Friday ahead of the game on Saturday. Police have been informed," a spokesman told the Sun Sport.
British media also reported that Palace's assistant head groundsman Dean Waters had condemned the vandals and revealed their error.
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"40,000 pounds worth of damage on our coach thinking it was the Boro coach. Nice one! #cpfc," Waters tweeted, before changing his privacy settings so that the post was no longer available to the public.
(Reporting by Shravanth Vijayakumar in Bengaluru)
