The Magpies have agreed a £6.97m fee - rising by another £1.7m in bonuses - for the 27-year-old striker, who scored 16 goals in Ligue 1 last season.
However, Aulas has complained to the French Professional Football League (FPFL) that rivals Marseille have made an illegal approach for the player.
"Mr Aulas says that during negotiations between the representatives of Bafetimbi Gomis and Newcastle, Olympique de Marseille intervened to make contact with the player and his agents without warning Lyon," read an official statement released by the FPFL.
"As a result, if the negotiations with Newcastle should collapse, it would be Marseille's fault."
Gomis joined Lyon from arch-rivals Saint-Etienne in 2009.