Melchie Dumornay scored an 82nd-minute goal to give Lyon a 2-1 advantage against Arsenal in the first leg of their Women's Champions League semi-final at Emirates Stadium.
The Gunners are looking to reach their first Champions League final since they won the competition - then known as the Uefa Women's Cup - in 2007.
Their bid for a first European trophy in 18 years suffered a blow in the 17th minute as Kadidiatou Diani's cool finish put eight-time champions Lyon in front.
Lyon's celebrations were initially cut short by the offside flag, but they resumed when the video assistant referee judged Emily Fox to have narrowly played Diani onside before the France winger slotted past Manuela Zinsberger.
Roared on by the home crowd, Arsenal surged forward in search of an equaliser and were handed a lifeline with 15 minutes remaining when the VAR advised the referee to review a challenge by Christiane Endler on Leah Williamson.
After watching the Lyon goalkeeper make slight contact with Williamson's head on the pitchside monitor, referee Ionela Pesu controversially awarded a penalty.
Mariona Caldentey, who won the Champions League with Barcelona last year, stepped up to the spot and calmly fired home to level, sending the Emirates crowd into chaos.
But the jubilant scenes were short-lived as Lyon restored their lead four minutes later when Dumornay powered between Fox and Steph Catley before finishing over the onrushing Zinsberger.
The second leg will take place at Parc Olympique Lyonnais on 27 April, with the winner of the tie facing either Chelsea or Barcelona in the final in Lisbon on 24 May.