Tomas Horava took advantage of some poor defending from the Ligue 1 side in the opening minutes to claim an early lead for Plzen before the score was levelled by Gueida Fofana 10 minutes later.
Alexandre Lacazette gave Lyon the lead early in the second half before Arnold Mvuemba claimed a valuable goal ahead of the trip to the Czech Republic for the second leg with Fofana's second adding gloss to the win.
Plzen got off to the perfect start when they scored in the second minute. Jan Kovarik's cross found Horava unmarked in front of goal and he headed past Lyon keeper Anthony Lopes with ease.
Lyon then went on to dominate play but equalised rather fortunately through Fofana after Steed Malbranque's corner hit him on the knee and deflected into the net.
Lacazette fired wide in the 21st minute before Stanislav Tecl missed the target at the other end after dispossessing Milan Bisevac and rushing towards goal.
Plzen's David Limbersky then forced a good fingertip save from Lopes just before the break as the teams left the field all square.
However, it did not stay that way for long in the second half as Lacazette powered a low strike into the net after Malbranque's ball left him in the clear with Mvuemba chesting down to fire beyond keeper Petr Bolek in the 61st minute for a 3-1 lead.
There was no luck involved for Fofana's second goal, as he slid the ball in from Lacazette's cross from the right to put Lyon within touching distance of the quarter-finals.