Fellaini left in the 29′ after getting treatment on his knee, with the Belgian FA, as well as Belgium Manager Roberto Martinez voicing fears that the attacking midfielder had suffered ligament damage.
Fellaini's withdrawal was clearly felt as it allowed Bosnia to equalise, but the already-qualified Belgium went on to win 4-3 in the end.
The injury does, however, rule him out of the clash with Liverpool this weekend as well as the Champions League tie with Benfica in Lisbon the following week.
However, the injury does mean Fellaini will miss United's Premier League trip to rivals Liverpool on Saturday.
Mourinho had bemoaned the loss of the lanky Belgian for his side's victory in Russian Federation, and won't be too pleased with the news of his latest injury ahead of next weekend's big clash at Anfield.
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Belgium manager and utter fraud Roberto Martínez did not sound hopeful: "We are all anxious about Fellaini".
Even though the Belgian ace may have avoided any major cruciate ligament damage, his sprained Medial Collateral Ligament (MCL) will give Mourinho and the Red Devils' fans a major headache. "Ligaments left knee. More news tomorrow", it said.
Belgium rested fellow United player Romelu Lukaku for the Bosnia clash after he picked up an ankle injury. Four goals from 8 games in all competitions have equaled the number of goals scored by Fellaini last season from 47 parties.
His injury will undoubtedly cause Jose Mourinho a headache.