Strasbourg enter their home showdown with Rayo Vallecano currently 1-0 down after Alemao's 54th-minute strike in the first leg.
But if the Ligue 1 side are to overturn the deficit and reach the final in Germany, they will have to do it without Emegha.
O'Neil confirmed in his press conference that the 23-year-old suffered a hamstring injury that will rule him out of the final two league matches of the season, and Strasbourg's second leg against Vallecano.
The former Wolves boss did offer a glimmer of hope that he could return to the final - if they get there - stating there's "maybe a chance" of him featuring. But as it stands, he may have played his final game for the club.
Emegha's permanent move to Chelsea on a seven-year contract was confirmed back in September, and the forward has since endured a frustrating campaign with injuries.
The Netherlands international has only made 18 appearances in all competitions this term, finding the net eight times.