Ryoya Morishita opened the scoring for Legia in the 17th minute, followed by Mateusz Szczepaniak's strike in the 77th.
An own goal by Omonia's Andronikos Kakoullis in the 86th minute sealed the win for the visitors.
After four rounds of fixtures, Legia sit in second place in the Conference League standings, with 12 points and no goals conceded. Chelsea lead the group on goal difference.
The Polish side began their campaign with a 1-0 home win over Spanish team Real Betis. They followed it up with a 3-0 away victory against Serbian club TSC Bačka Topola and a commanding 4-0 home triumph over Belarusian side Dinamo Minsk on November 7.
Legia's next group-stage fixture will see them host Switzerland's Lugano in Warsaw on December 12, Polish state news agency PAP reported.
Meanwhile, fellow Polish club Jagiellonia Białystok played out a dramatic 3-3 draw with Slovenian side Celje in their fourth Conference League group-stage match on Thursday.
Jagiellonia, with three wins and one draw from their four games, sit third in the standings with nine points, trailing Chelsea and Legia by three
Both Polish teams have two remaining matches in the group stage, which concludes on December 19.
The top eight sides in the league phase of the new-look Conference League will qualify automatically for the knockout stages, while the teams finishing in ninth to 24th place will compete in a two-legged play-off to secure a place in the last 16 of the competition.
Teams ranked 25-36 will be eliminated from the competition, run by European football governing body UEFA.
Source: IAR, PAP, polskieradio24.pl