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Cornet's big moment came in the 23rd minute as Lyon forward Karl Toko Ekambi broke free from the City backline.
Following a spectacular tackle from Eric Garcia to dispossess Toko Ekambi, Cornet pounced as he fired a shot past Ederson and into the back of the net.
The goal gave Lyon a 1-0 lead early, but it wasn't the first time Cornet got the better of the City defence.
Cornet previously terrorised the City rearguardin the 2018-19 Champions League, as Lyon faced off with Pep Guardiola's side in the group stage.
After scoring the first of two goals in a 2-1 win at the Etihad in the first match of the group stage, Cornet fired two more in their second clash, a 2-2 draw back in France.
With Saturday's goal, Cornet now has four goals against City over the last two seasons, giving him the joint-most goals against the club in the Champions League since Guardiola took over in 2016.
Only Messi has scored the same amount since the Catalan arrived at the Etihad, with the Argentine firing four times as Barcelona faced off with his former manager back in the group stage in 2016.
Cornet has not had a particularly prolific campaign for Lyon, having fired only four goals in 22 Ligue 1 matches this season.
The Ivorian international joined Lyon from Metz in 2015, having made at least 36 appearances in each of his first five full seasons with the Ligue 1 side.
Internationally, Cornet has scored four goals while earning 18 caps for the Ivory Coast, earning a call-up for the 2019 African Cup of Nations.
Lyon finished the 2019-20 campaign seventh in Ligue 1 after the French season was halted due to the coronavirus pandemic.