The Greece international suffered a cut above his eyebrow in second-placed Schalke's 3-2 defeat at Hoffenheim in the Bundesliga on Saturday.
"He could not do any headers in training," coach Huub Stevens told reporters on Monday.
Schalke are top of the group on seven points after beating Arsenal 2-0 in London last month. The English club are second on six with Olympiacos on three and Montpellier on one.
Stevens hinted he may freshen up his side following a busy spell in three competitions.
"I still do not know what team I will field against Arsenal. It could be that I will make some changes but this has nothing to do with the Hoffenheim defeat. We have to win back that freshness," he added.
"Arsenal played well despite their weekend defeat to Manchester United. I have carefully watched the past few matches of our opponents and let's just say we are well prepared."