The Brazil international had the ball in the back of the net in the 91st minute, but VAR adjudged there to have been a handball in the build up.
It ended City’s 15-game winning run in the Premier League, in what was an enthralling encounter at the Etihad.
Raheem Sterling opened the scoring for Pep Guardiola’s side with his fifth goal of the campaign, before Erik Lamela restored parity soon after.
Kevin de Bruyne provided his second assist of the game in teeing up Sergio Aguero, but City’s hard work was cancelled out by substitute Lucas Moura’s header - the Brazilian scoring with his first touch.
Guardiola looked to the bench for further firepower, with Gabriel Jesus, David Silva and Riyad Mahrez all brought on, but the former’s strike was chalked off after Aymeric Laporte was ruled to have handled the ball in the build-up.
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