The 30-year-old scored a hat trick on the night – which completed a 3-2 aggregate victory – but was forced off in the final moments of the match, much to the concern of the home bench.
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The Red Devils overturned a 2-0 deficit from the first leg to progress to the quarterfinals but the Scot could potentially be without his match-winner for at least the upcoming Premier League games against West Ham and Manchester City.
However, Moyes told Sky Sports after the game: "It doesn't look that bad. I've just gone in to see him just now. He's certainly had a knock in and around the knee area, so we don't know exactly. Could be just [that he took] a knee in the back of his knee.
"Not many people score a hat trick in Champions League football," he added of the Dutchman's performance, "and it was a great hat trick as well.
Danny Welbeck and Wayne Rooney also started against the Greek side, who had just clinched their 41st domestic title, and could step into the breach should it be required.
Javier Hernandez has found himself out of the starting lineup in recent weeks, amid links with a summer transfer, but the Mexico international could also be called upon.