Ramsey may have played his last game for Arsenal after he pulled up feeling the back of his thigh midway through the first-half.
The 28-year-old will join Juventus as a free agent this summer, bringing his 11-year stay at Arsenal to an end.
When quizzed about the injury, Emery said: “I don't know. It's a muscular injury. Normally it's some weeks out of the team.
“It's a shame because he was in a very good moment, working very well, but we have other players waiting for their opportunity.”
Arsenal scored shortly after Ramsey was withdrawn, with their 3-0 aggregate victory setting up a semi-final against Valencia.
Emery added: “(I am) proud of my players and of our supporters who came here to be with us.
“This was a game with a big team, in a big atmosphere. We started well, the first half was good, we scored the goal and then we worked very well in the second half. Over the two matches we deserved to win against Napoli.”
Assessing the semi-final against Valencia, a team he managed from 2008-2012, he said: “They are a very good team, great players. It's a good match for us.”
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