The French giants, who have lifted the trophy in the last four editions of the tournament, will be looking to make it five in a row and only have two more matches between themselves and the title.
It was an admirable performance from Germany's number two side, FC Bayern, but they were just edged out by Jean-Luc Vasseur's side, whose strength in every position on the pitch was evident.
Lyon started the game the stronger of the two sides from the off, with Eugenie Le Sommer impressing on the left-wing, linking up the play towards Nikita Parris up top. Lyon remained on top and dominated the possession, but Bayern's defence proved difficult to break down.
The first real chance of the night fell for FC Bayern in the 22nd minute. After Hanna Glas found herself in acres of space on the right, she played in a looping cross towards Lea Schüller but it was just too far away for the 22-year-old to connect with it.
It took until the forty-minute mark for the reigning champions to take the lead. Le Sommer hooked the ball over the defence towards Nikita Parris in the middle who guided a header into the back of the net, but as she did so she was met by the hands of FC Bayern goalkeeper Laura Benkarth who received a yellow card. Despite what looked like a rather nasty head injury, Parris was able to get up and keep on playing.
Dzsenifer Maroszan picked up a yellow card in the 55th minute after a late challenge on fellow German Sydney Lohmann.
After Cascarino was brought down just outside of the box in the 58th minute, Lyon were handed a free-kick. Amel Majri stood over the ball, and her outswinging attempt was met by the hand of Benkarth, but it was not enough to stop it from reaching the back of the net.
In an attempt to bring on fresh legs and find a way back into the game, Lineth Beerensteyn and Lea Schüller were replaced by Viviane Asseyi and Jovana Damnjanović.
It didn't take long for Bayern to find a way back into the game. Carolin Simon fired in a low curling free-kick in the 64th minute from the left-wing, which went under the wall, dissected the defence and could not be met by an onlooking Bouhaddi.
Lyon refreshed their team shortly after, with Eugenie Le Sommer and Nikita Parris replaced by Sakina Karchaui and Jodie Taylor.
With fifteen minutes left to play, Bayern's top scorer in the Frauen-Bundesliga this year, Jovana Damnjanović, saw herself brought down and had to be carried off after a knee injury. She was replaced by veteran Simone Laudehr.
FC Bayern came close to equalling the scoring in the 80th minute as Sydney Lohmann's effort rattled the crossbar, and shortly after Lohmann was taken off alongside Hanna Glas and replaced by Sarah Zadrazil and Amanda Ilestedt respectively.
Aiming to see the game out, full-back Selma Bacha was brought on in place of Maroszan for Lyon.
Glas impresses for FC Bayern
Playing against a strong Lyon side, it was always going to be an uphill battle for Bayern, but Swedish defender Hanna Glas, who joined the Bavarians from PSG earlier in the summer, was impressive.
The central defender played a crucial part in Bayern's side as they aimed to keep Lyon out, and in the end their hard work was only undone by a clinical free-kick from Majri.
Le Sommer and Cascarino cause havoc
Eugenie Le Sommer, who provided the assist for Lyon's first goal, and Delphine Cascarino were impressive for Lyon and proved troubling for Bayern's defence until the former was taken off in the 65th minute.
The French duo regularly swapped wings, causing havoc for the two full-backs. This resulted in a number of opportunities for Lyon, with Cascarino missing a clear-cut chance that saw her go one-on-one only for her shot to be saved from close range.
It was Cascarino herself who earned the free-kick that provided Lyon with the chance for her side's second goal, weaving her way into the defence before being brought down just outside of the box.
Player of the match - Eugenie Le Sommer
As is often the case with Lyon, there was not necessarily any one player who stood out above the rest, with every player on the team playing at an incredibly high standard.
However, Le Sommer's impressive assist for the first goal, coupled with her attacking play on the wing for the first sixty minutes, saw her be one of the top players in the game.