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Amandine Henry, Eugenie Le Sommer and Ada Hegerberg all scored in a crazy first period of extra time to stun Wolfsburg, and substitute Camille Abily later made sure of the victory.
The German champions had taken a 93rd-minute lead courtesy of their Danish star Pernille Harder, only for influential midfielder Alexandra Popp to be sent off almost immediately after.
Lyon are the first side to lift the trophy three years running, and also set a new record by winning the tournament for the fifth time overall.
It has already been a glorious first season in charge for coach Reynald Pedros, with Lyon having won a 12th consecutive French league crown -- they can still make it a treble with the French Cup final to come against Paris Saint-Germain.
"Over the whole game we definitely deserved the win," said Lyon's England star Lucy Bronze.
"I don't think we were quite ourselves in the first half and it took us a while to really get into the game and play the way we know we can.
"Wolfsburg tired a bit at the end but I think we showed our class with all the goals that we scored."
The extra-time drama came after a tense 90 minutes in the third final confrontation between these sides in six seasons.
In 2013, Wolfsburg triumphed 1-0 in London for their first of back-to-back titles. Lyon gained their revenge in 2016, winning on penalties.
This encounter was watched by over 14,000 in the leafy setting of Kiev's Valeriy Lobanovskyi Dynamo Stadium, just 48 hours before Real Madrid and Liverpool clash in the men's final across the Ukrainian capital.
Lyon have almost become the women's equivalent of Real, with the Spanish side also going for a third successive Champions League crown on Saturday.
Shell-shocked
They had enjoyed the better of the chances in normal time, and felt they were denied a goal in the second half -- an Henry header was cleared from possibly behind the line, and without goal-line technology nothing was given.
"I think it was a goal but the referee didn't see it," said captain Wendie Renard.
Lyon then fell behind early in extra time when Harder's strike from outside the box found the net via a deflection off Renard.
The German double winners were euphoric, but they were brought back down to earth within two minutes of that when Popp was shown a second yellow card.
Popp watched on in horror as France midfielder Henry drilled in the equaliser in the 98th minute, and 60 seconds later substitute Shanice van de Sanden set up Le Sommer to put Lyon in front.
It was 3-1 before half-time in extra time as Van de Sanden provided another assist, this time for the prolific Norwegian Hegerberg.
With Wolfsburg shell-shocked, veteran midfielder Abily came off the bench to sidefoot in the fourth.
