Alexandre Lacazette's powerful late strike changed the balance of the tie, meaning the Giallorossi now must score at least twice at the Stadio Olimpico next weekend if they are to progress.
Luciano Spalletti's side led at half-time - and deservedly so - after Mohamed Salah and Federico Fazio had more than cancelled out Mouctar Diakhaby's opener, but a second half rally from Les Gones would prove their undoing.
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Corentin Tolisso scored minutes after the break to restore parity, before substitute Nabil Fekir broke that deadlock with a solo strike 15 minutes of time.
Lacazette then rifled home in injury time, increasing the challenge that now will face Roma in the second leg.
After opting to start Diego Perotti and Stephan El Shaarawy in the weekend defeat to Napoli, Spalletti restored Mohamed Salah to the starting line-up for this one - perhaps with one eye on the effect of his pace on the counter-attack.
Daniele De Rossi captained the side, with Juan Jesus slotting in defence alongside Federico Fazio and Kostas Manolas due to the suspension of Antonio Rudiger.
5' - Early chance for Roma! Nainggolan hits a powerful drive from the edge of the box but Lopes parries away!
9' - Goal for Lyon. Diakhaby meets the inswinging free-kick and turns home from close range... 1-0.
13' - Jesus makes an important block to deny Valbuena as he bears down on goal...
20' - GOAL! ROMA LEVEL! Hesitation and then a slip from Diakhaby allows Salah to run onto the long ball ... and he slots home under Lopes with aplomb! 1-1!
31' - Another chance! Strootman runs onto the Salah pass but the defender gets a key block in as the Dutchman shoots!
33' - GOAL! ROMA HAVE THE LEAD! Fazio meets De Rossi's inswinging cross from six yards out ... Lopes never stood a chance! 1-2!
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48' - Goal. Lyon are level. Tolisso gets space 20 yards out and rifles the ball inside the far post... 2-2.
69' - Alisson makes three saves in relatively quick succession to deny Gonalons, Tolisso and Valbuena.
74' - Goal. Lyon lead. Substitute Fekir shows some quick feet in the box before slotting a curling shot inside the far post. 3-2.
90' - Emerson goes for goal from 25 yards but Lopes has it covered. Four minutes of injury time to come.
90' +3: Goal. Lyon double their advantage at the death. Lacazette finds the top corner from 18 yards out. 4-2.
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“We need to stay positive and believe in ourselves. I’m convinced that this team, this group, can win the return leg. That’s why it’s key that all the Roma fans come to the stadium next Thursday and are there with us."
- Federico Fazio
The Giallorossi are back in Serie A action at the weekend, as they travel to face Palermo in the late kick-off on Sunday evening.
They are then back at the Stadio Olimpico on Thursday - looking to turn around this deficit as Lyon arrive in the capital for the return leg.
Goalscorers: Diakhaby (5'), Tolisso (47'), Fekir (74'), Lacazette (90'); Salah (20'), Fazio (33')
Olympique Lyon: Lopes; Morel, Mammana (Fekir), Diakhaby, Rafael (Jallet); Gonalons, Tolisso, Tousart; Valbuena, Lacazette, Ghezzal (Cornet).
Roma: Alisson; Jesus, Fazio, Manolas; Emerson, Strootman, De Rossi (Paredes), Peres; Nainggolan (Perotti), Salah; Dzeko.
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