The full extent of the defender's injury has yet to be determined but there are already reports in Spain emanating that the Catalan will be out for the entire season
The 20-year-old, who has recently been linked with a move to Ajax, sustained the injury shortly after coming on as a half-time substitute during the game at the Imtech Arena.
"Marc Muniesa suffered a possible tear of the anterior cruciate ligament in his right knee," Barca confirmed in a statement.
"The Catalan defender will undergo further tests on Wednesday to confirm the exact extent of the injury."
Barca boss Tito Vilanova admitted Muniesa's misfortune had taken the gloss off his first formal outing since succeeding Pep Guardiola as coach.
"It looks a bad injury," he lamented. "[But the game] was what it had to be; an intensive workout, and I think that overall we played well.
"For me, this was a special game, having taken to the bench as head coach after four years as assistant."
Dani Alves opened the scoring for Barcelona early on and although Tolgay Arslan levelled matters midway through the first half, Gerard Deulofeu scored what proved the winner on 38 minutes.