The 19-year-old signed for the Gunners from Les Verts in a £27m deal last summer, but returned to France on loan for the season as part of the deal.
Ligue 1 was cancelled in April due of the coronavirus pandemic but the Coupe de France final between Saint-Etienne and Paris Saint-Germain will take place on July 24, and it was hoped a deal could be agreed to extend Saliba's loan until after the match.
But the French club released a statement on Wednesday confirm the defender had returned to north London after Arsenal made ‘unacceptable demands during negotiations’.
The Gunners have hit back though, with an official club statement reading: “Throughout our discussions with St Etienne, our aim has been to protect the welfare of William Saliba as well as the interests of Arsenal Football Club, while honouring the terms of the loan.
“Despite the loan ending on June 30, we were willing to find a way for William to play in the [French] cup final on July 24, despite having no contractual obligation to do so.
“As William is returning from injury, we asked that St Etienne follow a clear training plan with William in close collaboration with us, to ensure he is fully fit for the start of next season.
“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.”
The Gunners also revealed they would have been left at a financial disadvantage if Saliba played in the final.
According to French football expert Julien Laurens, a 17th start of the season would have cost Arsenal an extra €2.5m. St Etienne were asked to cancel that clause if Saliba was to start, but the French club refused.
“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,” Arsenal’s statement continued.
"We know this is a disappointment for William but he understands we are working to protect his long-term interests and those of Arsenal.”
The news comes after Gunners boss Mikel Arteta admitted that Saliba deserved to play in the final, saying: “He has earned the right to play in that final if the manager wants to do that.
“I think we have to give him the opportunity to do that, to enjoy that and we can have him after that.”