Turkish winger Cengiz Under and Harvey Barnes scored to give their team the win at the King Power Stadium.
Under netted his first goal for the Foxes since moving to the Premier League side on a season-long loan from Roma.
Braga defeated Zorya Luhansk 2-0 at home in another group match.
Leicester City and Braga have each collected 13 points, but the English side finished the group at the top with a better head-to-head record.
Zorya Luhansk are third with 6 points and AEK Athens sit at the bottom of the group with 3 points.
The group stage in the Europa League ended as a total of 24 clubs from 12 groups booked their tickets for the knockout stage.
Roma, Young Boys, Arsenal, Molde, Bayer Leverkusen, Slavia Prague, Rangers, Benfica, PSV Eindhoven, Granada, Napoli, Real Sociedad, Leicester City, Braga, Milan, Lille, Villarreal, Maccabi Tel-Aviv, Tottenham, Royal Antwerp, Dinamo Zagreb, Wolfsberger, Hoffenheim and Crvena Zvezda moved to the Europa League knockouts.
In addition to these 24 teams, Salzburg, Shakhtar Donetsk, Olympiacos, Ajax, Krasnodar, Club Brugge, Dynamo Kiev and Manchester United came third each in their Champions League groups to secure their Europa League last 32 tickets as well.
The last 32 draw will be held on Dec. 14.
Week 6 results in Europa League:
Group A:
CSKA Sofia - Roma: 3-1
Young Boys - Cluj: 2-1
Group B:
Dundalk - Arsenal: 2-4
Rapid Wien - Molde: 2-2
Group C:
Bayer Leverkusen - Slavia Prague : 4-0
Hapoel Beer-Sheva - Nice: 1-0
Group D:
Standard Liege - Benfica: 2-2
Lech Poznan - Rangers: 0-2
Group E:
PSV Eindhoven - Omonoia: 4-0
PAOK - Granada: 0-0
Group F:
Napoli - Real Sociedad: 1-1
Rijeka - AZ Alkmaar: 2-1
Group G:
Braga - Zorya Luhansk: 2-0
Leicester City - AEK Athens: 2-0
Group H:
Sparta Prague - Milan: 0-1
Celtic - Lille: 3-2
Group I:
Maccabi Tel-Aviv - Demir Grup Sivasspor: 1-0
Group J:
Tottenham - Antwerp: 2-0
Ludogorets - LASK: 1-3
Group K :
Wolfsberger - Feyenoord : 1-0
Dinamo Zagreb - CSKA Moskova: 3-1
Group L:
Slovan Liberec - Crvena Zvezda : 0-0
Hoffenheim - Gent : 4-1
