PSG now face Lens in the last eight, the club they beat in last season's final.
Luyindola scored his first goal on the half-hour from a pass by Mateja Kezman and netted his second six minutes later.
In Wednesday's other fourth round game, Le Havre won their all-Ligue 1 tie against Rennes 2-1 thanks to a penalty converted by Jean-Michel Lesage in extra time. Le Havre now face Nice.
Lyon shocked by Metz
On Tuesday, seven-times French champions Lyon were knocked out by second-division Metz.
All the quarter-final ties will be played on January 13.
'Hopefully the president we choose will be OK' - Guardiola on Barca elections
The award for worst penalty of the season goes to... Wout Weghorst