The 19-year-old was training with Claude Puel's team ahead of Saint-Etienne's clash with Pairs Saint-Germain on July 24.
Saint-Etienne have now ruled him out of the contest, however, claiming a deal to extend his stay in France fell through because Arsenal attempted to "impose unacceptable financial and sporting conditions," according to a translation of the club's statement by Get French Football News.
Saliba's omission may come as a shock to Arsenal boss Mikel Arteta, who said earlier Tuesday he was hopeful Saliba would remain in France to compete in the final before arriving in north London.
"He has earned his right to play that final if their manager wants to do that," Arteta said before talks fell through. "So I think we have to give him the opportunity to do that, to enjoy that, and we can have him after that."
Arsenal signed Saliba to a five-year contract last summer after reaching an agreement with Saint-Etienne reportedly worth £27 million (€30 million).
Arsenal responded with a statement Wednesday saying, "To our surprise we were unable to reach agreement to this plan which was proposed by our medical experts, and we are simply not prepared to risk the welfare of an Arsenal player.
"While it was not our primary concern, and ultimately not relevant as our training plan was not accepted, we also expected not to be financially disadvantaged by extending the loan. This was also not acceptable to St Etienne."
The Premier League side agreed to loan him back to Saint-Etienne for the 2019-20 campaign. Saliba made 28 appearances before the Ligue 1 season was canceled due to the coronavirus pandemic.
The French Football Federation announced last week that the Coupe de France final had been rescheduled.
Saint-Etienne have been preparing for the club's first appearance in the final since 1982. The French side last won the competition in 1977.