Cengiz Under equalised just six minutes after Jan Kovarik had opened the scoring at the Doosan Arena midway through the second half - only to see Tomas Chory steer home a header not long after that to ultimately decide the game.
Substitute Luca Pellegrini was sent off for Eusebio Di Francesco's side in the dying moments, after picking up a second yellow card.
The Giallorossi had already qualified for the knockout stages of the competition as runners-up, but failed to round off this phase of the campaign with a win.
They are next in action on Sunday evening, as Genoa come to the Stadio Olimpico on Sunday night.
The draw for the last-16 of the Champions League takes place on Monday.
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