The France international had looked set to leave the club for the Premier League with Newcastle coming close to striking a deal.
But, just as a move to Swansea failed to materialise, the proposed deal with the Magpies also collapsed.
A number of Bundesliga and Turkish clubs also showed an interest but now Gomis, who has just 12 months left on his contract, is set to stay until January at least.
Gomis will now be invited back into the squad after being sidelined by the club's management and will be offered a new deal.
Lyon president Jean-Michel Aulas said: "We have to face facts, there isn't an offer that Bafe has accepted despite (interest from) the English and the Turks and Lyon need a player like him.
"It was logical that Bafe would not reach the end of his contract, but if it is not possible (to extend) we have no more time to reinforce the team, so he will be our reinforcement."