The midfielder was forced off after 29 minutes of his side's 4-3 World Cup qualifying win over Bosnia-Herzegovina on Saturday.
Head coach Roberto Martinez admitted it was likely he had damaged a ligament and there had been concerns he had suffered a tear.
@Fellaini is out for a couple of weeks & #BELCYP . Scan left knee injury (MCL sprain). Get well soon Marouane ! #RoadtoRussia pic.twitter.com/jozfljXOCl — BelgianRedDevils (@BelRedDevils) October 8, 2017
However, tests have revealed he has only sprained the medial collateral ligament of his left knee and is likely only to be out of action for "a couple of weeks", with Belgium confirming the news via their official Twitter account.
It is a blow nonetheless for United, who must take on fierce rivals Liverpool in the next Premier League match without either Fellaini or Paul Pogba in central midfield.
He could also miss the visit to Benfica in the Champions League as well as United's trip to Huddersfield Town that follows on 21 October.
He is likely to be replaced by last season's Player of the Year, Ander Herrera, while club captain Michael Carrick could also come into contention for a start.
Fellaini has scored four goals in all competitions for the club in a resurgent run of form this season, prompting speculation he will be offered a two-year extension to his contract, which expires in 2018.