An early goal from Marc Janko set the Turkish side on course to reach a healthy tally of seven points and Olcan Adin's free-kick defused a late Legia fightback to confirm the win.
News of Lazio's goalless draw at Apollon Limassol then filtered through to the home fans after the final whistle, a result that sees Trabzonspor go two points clear of their Italian rivals in the standings.
Austrian striker Janko has found goals hard to come by since leaving Porto last year but he only needed seven minutes to open the scoring against Legia.
His first close-range effort may have been stopped by Wojciech Skaba but after the rebound came back to his feet in the ensuing scramble, he tucked home.
Chances were at a premium for the rest of the first half but Jakub Kosecki and Tomasz Brzyski both tested home goalkeeper Onur Kivrak.
There was little to cheer after the break either and it was not until the 57th minute that Paulo Henrique forced a brave block from Legia's Jakub Rzezniczak.
Vladimir Dvalishvili sparked the game back into action as time ticked away, his snapshot unsettling Kivrak, whose poor clearance fell to Dominik Furman in a good position.
The Polish midfielder picked his spot from 12 yards but came up against a better save from the recovering Kivrak.
Just when it looked like the visitors might force their way back into the tie, Trabzonspor scored their second goal.
A bad foul on Yusuf Erdogan from Brzyski in the 82nd minute allowed Olcan to step up and steer a free-kick just beyond the reach of Skaba.