Martinez has recently heaped praise on the 24-year-old, who has excelled with United this season.
He was forced off in the first of those games when he landed awkwardly after challenging former Manchester City striker Edin Dzeko for a ball in the air.
However, Martinez has since confirmed that Fellaini suffered knee ligament damage, which is likely to keep him out of action for a lengthy spell. "We fear that there's ligament damage", he said after the match.
The England worldwide then opted for Patrice Evra at left-back, and Paul Scholes, Michael Carrick, Ryan Giggs and Paul Pogba in a midfield four, with Wayne Rooney and Marcus Rashford as his two strikers.
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In a post on social media, Belgium said Fellaini has had a scan and will be "out for a couple of weeks".
Fellaini is set to miss United's trip to Anfield to face Liverpool on Saturday.
However, he has since been declared as fit by Martinez, and could be in line to feature versus Cyprus tomorrow night. The Belgian boss is quoted as saying by the Daily Mail.
Romelu Lukaku, Fellaini's club and global team-mate, did not play against Bosnia-Herzegovina because of an ankle problem. Also, his injury has left Mourinho short of options as Paul Pogba is already out, and Matic - who has played every single minute in the Premier League, has confessed that he is not 100% fit as well. "And no, I have not received a call from Mourinho".
"But there was nothing wrong in that respect so the relationship is very, very good with Manchester United as you would expect".