The French striker has agreed to the move, which is believed to be worth around £9m, although a delay in finalising the deal is expected.
"With one year left on his contract he has to be sold because an extension was not an option for us or him," said Aulas in quotes reported by the Newcastle Chronicle.
"I did not mean to cause any harm to Gomis on a personal level. I merely needed to sell him. We have accepted Newcastle's conditions and Gomis has accepted theirs too.
"It could still go haywire. There are minor issues which could cause problems. Either way, the deal won't be done for another eight days probably."
Gomis, who scored 16 goals in 37 Ligue 1 appearances last season, is likely to be the Magpies' first signing this summer.