Just when it seemed Arsenal would take three points from an unimpressive performance, they were denied at the last, the Brazilian defender Edmilson who was once coveted by Arsene Wenger, heading in a corner in the final minute.
Hard as it will be for Arsenal to take, it was no more than Lyon deserved, even if for all their long bouts of pressure they had failed to bring a serious save out of David Seaman.
Arsenal were never at their best after Dennis Bergkamp had put them ahead in controversial fashion in the 32nd minute. He was not penalised for a shove on Edmilson, who will feel justice was done when he nodded in Vikash Dhorasoo'scorner.
Arsenal may now need to take a point at Bayern Munich to reach the last eight. After six straight victories, including a 10 win at Lyon last week thanks to Thierry Henry's strike, Arsenal must have been confident of taking a further stride towards their first appearance in the quarter-finals of this competition.
Not that they can have expected an altogether easy night. Lyon had shown, particularly in the early part of the game in France, that they possessed dangerous pace and movement, and Arsenal were forced to cope without their captain, Tony Adams, who had a bad back.
That meant Wenger used his third centre-half pairing in as many matches, Gilles Grimandi partnering Oleg Luzhny.
At the other end the Arsenal manager was spoiled for choice, deploying Dennis Bergkamp alongside Henry and leaving Nwankwo Kanu on the bench for the first time in Europe this season.
Bergkamp showed some neat touches early on and, after Robert Pires sent a cross-shot wide, the Dutchman's cushioned header provided Ray Parlour with an opportunity he should have taken. To Highbury's dismay the midfielder, eight yards out, sliced his volley just wide in front of the watching England coach Sven-Goran Eriksson.
Not that Parlour was having a bad night. He and, in particular, Patrick Vieira began strongly and impressively in the centre of midfield as Arsenal took initial control.
But a series of crosses failed to bring the goal they craved and as a touch of sloppiness crept into Arsenal's play midway through the half, Lyon began to show the threat they could pose on the counterattack.
Jacques Santini's side, needing to avoid defeat to stand a realistic chance of progressing, had signalled their intent by starting with Sidney Govou wide on the right almost as a third striker and committed men forward whenever the opportunity arose.
Yet as Arsenal seemed to be losing their way they took the lead through Bergkamp in controversial fashion. The striker, chasing a Robert Pires through pass, appeared to shove Edmilson before breaking clear into the penalty area.
Somehow the Slovakian referee, Lubos Michel, decided there was no foul as the Brazilian defender hit the floor and Bergkamp ran on curl his shot beyond the oncoming Gregory Coupet.
ARSENAL: Seaman, Dixon, Grimandi, Luzhny, Cole, Ljungberg, Vieira, Parlour, Pires, Henry, Bergkamp. Subs: Manninger, Wiltord, Lauren, Malz, Upson, Vivas, Kanu.
LYON: Coupet, Deflandre, Edmilson, Muller, Brechet, Govou, Foe, Violeau, Laigle, Anderson, Marlet. Subs: Hugues, Dhorasoo, Loko, Delmotte, Malbranque, Linares, Cacapa.
Referee: L Michel (Slovakia)
