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."
Da Costa has suffered a difficult start to the 2024 season, failing to score points in the opening three races before finishing in the points in Sao Paulo and Tokyo.
His place in the Porsche team has come under scrutiny this week after it was revealed that Abt's Nico Muller had tested with the German manufacturer as a possible replacement to da Costa next season.
Post-race and before his disqualification, da Costa had said his victory "came at the right time" and relieved some of the pressure he had been facing.
Writing in response to FE's announcement of the penalty on Instagram, Da Costa said: "Throttle damper spring was an original part from Spark that was used all of last year and been removed from the rulebook without notification to the teams… how many other cars out there are on this spring?"
Porsche has declared its intention to appeal the disqualification, and has 96 hours to decide on whether to further pursue the matter.
Da Costa's disqualification means Rowland has inherited the win, which marks his and the team's first Formula E victory since the Briton's sole previous triumph in the all-electric championship at Berlin in 2020.
It is also the first win for Nissan since it took over full ownership of the team previously co-owned by DAMS in 2022.
Reigning champion Jake Dennis (Andretti) has been promoted to second, with Tokyo E-Prix winner Maximilian Guenther now taking a place on the podium for Maserati MSG.
