The Austrian international was playing his first match of the season following knee surgery at the end of last term.
But just over 45 minutes into his comeback, he clashed heads with Shane Lowry and was stretchered off.
Boro have now confirmed that Pogatetz has had surgery on the injury and will be sidelined for six weeks. It is a recurrence of the injury he picked up against Basel in 2006.
Pogatetz was brought back into the side along with Julio Arca - who was pleased to be handed a start by new boss Gordon Strachan.
"It's not easy when you are in and out, playing every few weeks, but to start and play most of the game helps me," he said.
Arca return"I just wanted to be back in the team and I told him I will play anywhere he wants me to, as long as I play.
"Training has been a bit different - more intense. He has tried to change things, which is probably hard to explain. He likes us to play football.
"Even at the end when we started to put balls in the box, he said we should have carried on playing football and waited for the right chance. He likes players to play, to pass the ball. He gave us the freedom to do what we do best.
"That suits me, even if I am playing in a position I have not played for a long time.
"We need time to get used to him and he will need time to get used to us. This week has been good because we have trained all week with him so we know what he is looking for.
"Hopefully things will work out. He wants to improve players, to make them play better to get promotion."