Da Costa had taken his first win of the season during the inaugural Misano E-Prix, but post race checks mean the Portuguese has been disqualified from the race result.
An FIA statement read: "At post-race scrutineering the Throttle Damper Spring mounted in car 13 during the race was not found in conformity with one of the three optional items declared in the GEN3 Spark Catalogue.
"The team manager and the representative of the manufacturer explained that since the beginning of season 9 they have not changed the Throttle Damper Spring.
"The team manager accepted that the sealed part, as shown in the attachment of the Technical Report 13 was mounted in car 13 and was sealed in the presence of the chief mechanic of the team.
"The team manager stated also that on the Spark list (pedals) the sealed part is not listed. He explained that normally changes of the Spark catalogue are highlighted so everybody can see the changes, but not the removements.
"The FIA Technical Delegate confirmed this procedure.
"The representatives of Spark confirmed that this part was listed on the part list of the Gen2 cars, but not on the current Gen3 car.
"They also confirmed that the removal of parts from that catalogue are not highlighted nor cancelled."
Source: Autosport