Emery was forced to replace Ramsey with Henrikh Mkhitaryan in the first half when the Welshman went down clutching the back of his thigh before limping off the pitch.
"It's a muscular injury and usually it is going to mean some weeks outside the team," Emery said. "I don't know if we'll see him again before the end of the season."
Arsenal, whose 3-0 aggregate win sealed a semi-final tie with Spanish side Valencia, host Crystal Palace in the Premier League on Sunday.
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(Reporting by Rohith Nair in Bengaluru; Editing by Peter Rutherford)
