Legia won in front of more than 24,000 fans at the Municipal Stadium in Warsaw on Thursday night, Polish state news agency PAP reported.
Defender Rafał Augustyniak gave the Polish side the lead on 14 minutes after a corner.
Playmaker Josué made it 2-0 to Legia from the penalty spot after half an hour.
The Polish team completed a double over their Bosnian opponents, after beating Zrinjski 2-1 in Mostar last month, public broadcaster Polish Radio's IAR news agency reported.
In Group E's other game on Thursday, Aston Villa beat AZ Alkmaar of the Netherlands 2-1.
After four rounds of matches, Legia top the group with 9 points, ahead of Aston Villa, also on 9, and Zrinjski with 3 points.
The 2023/2024 Conference League group stage matches are played between September 21 and December 14.
Group winners will progress to the round of 16, while group runners-up will face third-placed Europa League teams for spots in the round of 16, European football's governing body UEFA said.
The final of the 2023/2024 Conference League, Europe's third club competition, will be held on May 29, 2024 in Athens, Greece.
(pm/gs)
Source: IAR, PAP, Legia Warsaw, UEFA