Legia sealed their advance at the Municipal Stadium in Warsaw on Thursday night, Polish state news agency PAP reported.
Yuri Ribeiro opened the scoring on 34 minutes, and Blaž Kramer doubled Legia's lead with a header nine minutes from time.
Portuguese playmaker Josué created both goals.
Thanks to Thursday's victory, Legia finished second in Group E of the 2023/2024 UEFA Conference League with 12 points, one point behind Aston Villa of England, European football's governing body UEFA said.
The Polish Cup holders advanced to the Conference League knockout round playoffs.
They will play a third-placed team from the UEFA Europa League group stage for a spot in the last 16 of the competition, according to officials.
Legia will learn their opponents when the draw is made at UEFA headquarters in Nyon, Switzerland, on Monday, the PAP news agency reported.
The tie will be played over two legs on February 15 and 22, UEFA said.
Meanwhile, Polish champions Raków Częstochowa on Thursday went out of the 2023/2024 UEFA Europa League after losing 0-4 at home to Italy's Atalanta, which left them bottom of Group D, the PAP news agency reported.
(pm/gs)
Source: Polish Radio, PAP, UEFA