Mauro Icardi was preferred up top in place of the injured Kylian Mbappe, whilst Neymar Junior also started as PSG looked to bag a second cup in as many weeks.
A chance following the first eight minutes found the way of Neymar, but the Brazilian couldn't make the most of the situation with a wayward finish.
PSG were put to the test shortly afterwards, with Moussa Dembele accompanied by Memphis Depay threatening the breakthrough though Presnel Kimpembe cleared.
More persistence from the Ligue 1 champions afterwards almost led to a breakthrough, but Icardi along with compatriot Angel Di Maria couldn't profit as the half ended goalless.
Lyon immediately set on the attack straight after halftime with Maxwel Cornet picking out Houssem Aouar, who flashed wide of target.
A free-kick from 30-yards outside the area gave PSG a chance to breakthrough on 53 minutes, but Neymar was unable to trouble Anthony Lopes.
It was at this point that PSG manager Thomas Tuchel decided to change tactics, with Icardi and Idrissa Gueye sacrificed for Pablo Sarabia and Ander Herrera respectively five minutes later.
Neymar came close to stealing victory with a smart header off an equally smart delivery late on by Herrera, but Lopes tipped over as the match went to extra time.
Lopes dived to keep out Di Maria after the 96th minute, but Lyon went down to ten players in the second half of extra-time after Rafael da Silva saw red following a lunge on Di Maria in the last minute of the half.
The match was settled on a penalty shoot-out, as PSG ran out 6-5 victors after Bertrand Traore missed Lyon's decisive kick in sudden death.