The Polish side's Azerbaijani striker Mahir Emreli scored the only goal of the match in the 31st minute in Warsaw on Thursday night.
Two weeks earlier Legia defeated Spartak Moscow 1-0 away from home in the opening game of the Europa League group stage.
After two rounds of fixtures, Legia top the standings on a maximum six points, three ahead of Russia's Spartak.
The Polish champions will next play Italian side Napoli as part of their 2021/2022 Europa League campaign on October 21.
Legia reached the Europa League after a 2-1 qualifying win over Czech side Slavia Prague in late August.
Earlier that month, the Polish top-flight club saw its hopes of qualifying for the Champions League group stage crushed by Croatian side Dinamo Zagreb.
Source: TVP Sport, PAP, polskieradio24.pl