Juventus are at risk of losing the top spot but the Turin giants are now unbeaten in 19 home matches in UEFA competition
"We have to look at the positives, we've played another match with Lyon and we'll now go to Sevilla looking for a win. Then, we have Dinamo Zagreb at home," Allegri said.
"This draw has taken us a step closer to qualification."
But after another dominant display at Juventus Stadium, where the Turin giants are now unbeaten in 19 matches in UEFA competition, fans had reason to feel disappointed.
Two weeks after a late Juan Cuadrado strike secured a 1-0 win in France and reinforced top spot in Group H, Gonzalo Higuain stepped up to beat Anthony Lopes from the spot to give the hosts a 13th minute lead.
But Lyon refused to give in and Bruno Genesio's visitors were finally rewarded when Corentin Tolisso bundled the ball past Gianluigi Buffon from a long free kick with six minutes left on the clock.
"It gives us a small chance of qualification," said Tolisso. "Now we'll hope to win in Zagreb and hope that Juventus beat Sevilla so that we can challenge them for second spot at our ground."
Sevilla's win against Dinamo Zagreb means Juventus dropped to second place to sit two points behind the Spaniards and are now just four ahead of Lyon with two games remaining.
It has left Juventus at risk of losing the top spot, and the subsequent seeding that goes with it in the last-16 draw, to Sevilla.
But Allegri, who is bidding to steer Juve to a record sixth consecutive Serie A title this season, was unapologetic.
He underlined the numerous injury problems that have plagued his side of late and said a notable Juve lapse in the second period was simply due to fatigue.
Juventus are without strikers Paulo Dybala and Marko Pjaca due to injury, meaning Allegri had no-one to replace either Higuain or strike partner Mario Mandzukic.
When Higuain tired late in the second half, attacking midfielder Cuadrado came on, and Lyon scored minutes later as the visitors began to capitalise on Juve's fading powers.
Allegri added: "The front pair ran all night, and we didn't have any strikers to replace them. We could have perhaps done better on a few of the chances that we had.
"We came into this fixture following six intense games so it's normal the lads were tired.
"But for me this is a positive result. We're still fighting for first place in the group."
Lyon created the first chance of the night, Buffon forced to block Maciej Rybus's angled drive with both legs at his near post on eight minutes after a slick one-two with Alexandre Lacazette.
But it served as a wake-up call to the Italian champions, who should have wrapped up the match by the end of the first half after Higuain spurned a golden chance to add to his opener.
A slight push from central defender Mouctar Diakhaby on Stefano Sturaro as he awaited Higuain's through ball on the left was enough to send the Italian to the turf.
Referee Bjorn Kuipers pointed immediately to the spot and Higuain stepped up to send Lopes the wrong way.
Juventus were being given acres of space, but on more than one occasion, they failed to capitalise.
Claudio Marchisio's first-time effort shaved Lopes' near post before the half hour and then Higuain, to disbelief, skied a Mandzukic ball while alone in front of Lopes after the Croat had dispossessed Emanuel Mammana.
Lyon got a sniff of a goal when Andrea Barzagli got down to block Maxime Gonalons' drive after a puzzled-looking Sturaro somehow lost possession with the ball at his feet.
With just six minutes left on the clock, the stadium was stunned into silence when Buffon was well and truly beat by Tolisso's late header.