Ladislav Krejci fired the away for a 1-0 lead but Turkish international forward Yilmaz, who came on in the 77th minute, struck twice to bring the victory to the home side in Group H at Stade Pierre Mauroy.
Sparta Prague were reduced to 10 men after Ondrej Celustka was sent off in the 65th minute.
Following this victory, Lille moved to Europa League knockout stages with one match remaining after increasing their points to 11.
In other Group H match, Milan fought back from two goals down to seal a 4-2 comeback win over Celtic at San Siro.
Rogic and Edouard gave a 2-0 lead to Celtic but the home team salvaged all three points with Hakan Calhanoglu, Castillejo, Hauge and Brahim Diaz's goals to reach the knockout stages with 10 points.
Sparta Prague collected 6 points to be in third place while Celtic bottom the group with only 1 point.
Week 5 results in Europa League:
Group A
Cluj - CSKA Sofia: 0-0
Roma - Young Boys: 3-1
Group B
Molde - Dundalk: 3-1
Arsenal - Rapid Wien: 4-1
Group C
Nice - Bayer Leverkusen: 2-3
Slavia Prague - Hapoel Beer-Sheva: 3-0
Group D
Rangers - Standard Liege: 3-2
Benfica - Lech Poznan: 4-0
Group E
Granada - PSV Eindhoven: 0-1
Omonoia - PAOK: 2-1
Group F
AZ Alkmaar - Napoli: 1-1
Real Sociedad - Rijeka: 2-2
Group G
AEK - Braga: 2-4
Zorya - Leicester City: 1-0
Group H
Lille - Sparta Prague: 2-1
AC Milan - Celtic: 4-2
Group I
Qarabag - Maccabi Tel-Aviv: 1-1
Demir Grup Sivasspor - Villarreal: 0-1
Group J
LASK - Tottenham Hotspur: 3-3
Antwerp - Ludogorets: 3-1
Group K
CSKA Moscow - Wolfsberger: 0-1
Feyenoord - Dinamo Zagreb: 0-2
Group L
Gent - Slovan Liberec: 1-2
Crvena Zvezda - Hoffenheim: 0-0
