The Gunners were consigned to another excruciating second-placed finish in the top flight despite fighting back to beat the Toffees, who took the lead through a deflected Idrissa Gueye free kick before Takehiro Tomiyasu and Kai Havertz turned the tide.
Arsenal's win was meaningless in terms of the title connotations, though, as Manchester City triumphed 3-1 over West Ham United to secure a historic fourth straight top-flight title.
Prior to kickoff, Gooners were surprised to see Saka omitted entirely from the matchday squad, as the 22-year-old had seemingly shaken off the knock he sustained against Manchester United last weekend.
However, Arsenal quickly revealed that Saka had picked up a slight muscle problem in training, as Gabriel Martinelli deputised in an unfamiliar right-wing position against the Toffees.
Arteta insists Saka will be fine for Euro 2024
Explaining Saka's absence to the media before the game, Arteta said: "Unfortunately he picked up a small muscle injury in training. He wasn't available to play, but fortunately we have some great players, [Gabriel] Martinelli steps in."
Saka's latest fitness issue naturally raised a bit of concern over his chances of playing for England at Euro 2024, as Gareth Southgate prepares to name his preliminary squad on Tuesday, May 21.
However, speaking in his post-match press conference, the Spaniard emphatically responded with a simple "yes" when asked if the England winger would be available for this summer's championships.
Such news will come as a major relief to the Three Lions, who have two friendlies pencilled in with Bosnia-Herzegovina and Iceland on June 3 and 7 respectively before they head to Germany.
Placed in Group C of the tournament, Southgate's side begin their bid for glory against Serbia on June 16, before squaring off with Denmark on June 20 and Slovenia on June 25.
Arsenal, Brazil suffer worrying Gabriel Magalhaes blow
While Saka is only carrying something minor, a new concern has arisen over key centre-back Gabriel Magalhaes, who was forced off the pitch following a collision with Abdoulaye Doucoure on Sunday.
The duo engaged in a brief fracas for possession in the second half, in which Gabriel came off worse and fell to the turf clutching his shoulder, resulting in Doucoure being shown a yellow card.
A VAR review determined that no further punishment was necessary for Doucoure, but Gabriel was still feeling the effects of the battle and went down again clutching his shoulder before being taken off for Oleksandr Zinchenko.
It is still not clear how serious the defender's issue is, but his chances of competing for Brazil at this year's Copa America have been plunged into slight doubt.
The Selecao will face Costa Rica, Paraguay and Colombia in Group D of the competition from June 24 to July 2, and they also have two friendlies pencilled in against Mexico and the United States on June 8 and 12 respectively.