France forward Gomis struck from close range on 72 minutes to give Lyon 17 points from seven games.
Midfielder Moussa Sissoko exploited a blunder by the defence to put Toulouse in front after eight minutes but Lyon levelled through teenage striker Yannis Tafer seven minutes into the second half.
"I want to congratulate the players for the spirit they showed," said Lyon coach Claude Puel, who was without Argentina striker Lisandro Lopez and France defender Jean-Alain Boumsong through injury.
"We had quite a few problems but despite that we managed to fight back to earn a deserved win," Puel told French television channel Canal Plus.
"We were not serious enough defensively," said Marseille coach Didier Deschamps. "We led twice but we did not work hard enough and allowed them too much space.
"You can't say Valenciennes didn't deserve to win but my team certainly didn't do what I expect them to."
