The result saw Arsenal qualify from their group, but the achievement was overshadowed by Welbeck's setback.
Emery said: "It's the worst news tonight, this injury. It's clear that we are with him in these minutes. He was working well and he was having a good match. He had some chances too. His injury was with the mentality of the players. They [saw] it was a big injury. When you are playing football, when you are playing in competitive matches, it can happen. You don't want it to happen but this is our profession."
The manager also said: "Sporting are a very big competitive team, and organised. We spoke before and at half-time. Every Portuguese team is very competitive and today their commitment in the defensive moments was big. We needed to be calm and to create chances to score, but it's not easy on the pitch to make clear chances against them. I think this is the summary of the 90 minutes. It was difficult to create big chances against them. We created but it wasn't enough to win tonight."