While Fellaini was able to leave the stadium without the need for crutches, Martinez sparked concern after revealing fears over ligament damage post-match.
United have made an unbeaten start to the Premier League season, despite their injury woes, and now sit at the top of the pile alongside neighbours Manchester City.
As well as that, the Belgian will be unavailable for United's two Champions League games against Portuguese side Benfica, and a trip to Swansea City in the EFL Cup.
The full extent of Fellaini's injury won't be clear until he undergoes a scan, but he will play no part in Belgium's final group game on Tuesday against Cyprus.
United may breathe a slight sigh of a relief given their midfielder escaped without cruciate ligament damage which would have extended his time in the treatment room from weeks to months. "Ligaments, left knee. More news tomorrow".
It is a blow nonetheless for United, who must take on fierce rivals Liverpool in the next Premier League match without Fellaini or Paul Pogba in central midfield. Manchester United are now placed at second position in the Premier League with six wins and one draw in seven matches.
His withdrawal was clearly felt by Belgium as it allowed Bosnia to equalise in the game, but they went on to win 4-3 in the end to send a clear message to the rest of Europe ahead of next summer's World Cup in Russian Federation.
Marouane Fellaini has scored four goal for Manchester United in current season of Premier League.