Fabio Carvalho gave Liverpool the lead inside the opening minute, but a brace from Alexandre Lacazette either side of Bradley Barcola's effort handed Les Gones a deserved victory in 90 minutes.
The Reds would have the chance to secure a bonus point through the penalty shootout, but a missed effort from Calvin Ramsay proved to be the difference as Lyon claimed maximum spoils.
It took Jurgen Klopp's rejigged side all of 40 seconds to score the opening goal, as Mohamed Salah's effort was blocked following a flowing team move, but Carvalho was on hand to draw first blood from the rebound.
The Reds were the dominant force at the Al Maktoum Stadium in the early exchanges and had the chance to double their tally from the penalty spot on the 14 minute-mark, as Malo Gusto tripped Roberto Firmino.
However, the legs of Anthony Lopes denied Salah from 12 yards, although Liverpool continued to go in search of the insurance goal, albeit without Harvey Elliott as the youngster was taken off after just 28 minutes.
Moussa Dembele looked the biggest threat for Lyon and fired a powerful effort straight at Caoimhin Kelleher just before the 40-minute mark, but Laurent Blanc's side would find their reward at that exact point.
A horrendous mix-up between Kelleher and Andy Robertson saw the latter poke the ball past his onrushing goalkeeper under pressure from Lacazette, who then had the simple job of tapping home into an empty net.
A total of six half-time alterations were made by Klopp as the likes of Ramsay, Alex Oxlade-Chamberlain, Kostas Tsimikas and Adrian came on, and the former was a whisker away from restoring Liverpool's advantage right away, but Lopes touched his 20-yard drive wide.
However, it was Lyon's substitutes who would make the difference in the 65th minute, as Rayan Cherki embarked on a strong solo run before squaring for Barcola to fire Les Gones ahead.
A galvanized Gones side were enjoying themselves after Barcola's effort, and the 20-year-old then hit the post before Adrian denied Sael Kumbedi heading into the final 15 minutes.
The persistence of Blanc's side would pay dividends in the 83rd minute, though, as Lacazette was in the right place at the right time to finish into the roof of the net after Adrian parried a Kumbedi effort into his path.
Liverpool would be condemned to a two-goal defeat before the penalty shootout, where Maxence Caqueret, Tsimikas and Barcola netted before Lopes saved Ramsay's effort.
Cherki, Oxlade-Chamberlain, Tete and Naby Keita all converted their efforts before Damien Da Silva stepped up to try to score the winning penalty for Lyon, and the centre-back made no mistake to secure a perfect four points for Blanc's men.
Klopp's side now have five days to recover before they finish their Dubai Super Cup run against AC Milan, who tackle Arsenal on Tuesday, while Lyon return home to face Sochaux in Saturday's friendly.