Pogba has been criticised for his performances since his return to Old Trafford in 2017 despite helping the club win two major trophies in that time.
The France international was embroiled in a row with Liverpool legend Graeme Souness over his trophy haul but Fernandes has backed Pogba's ability.
"Paul is coming from a bad moment, because of the situation," he told the club website. "When he played also, the club and the team was not good, because the expectations are high for Paul, because Paul is a top player and Manchester United pay a lot for him, and expectations are a lot for him.
"Everyone expects this from Paul in Manchester, because they know he has the qualities for this. Also this is confidence in Paul. The team, we have a lot of confidence in Paul."
Since his move from Sporting CP in January, Fernandes has been unable to feature alongside Pogba who has been out of action since December after suffering metatarsal and ankle injuries.
United striker Ighalo said the club will become successful when both midfielders start playing together and Fernandes said he is excited for Pogba to return to the team.
"[I'm excited] a lot," he added. "I think we have a lot of good players in the midfield. I know Paul from Juve, because I played against him in Italy. And believe me, it's really hard to play against Paul.
"Because I play in midfield, I mark him. We play in the same line, so it's really difficult to play against Paul, because he has power, he has technique.
"It's difficult to find a player like Paul: big, strong and technical. It's difficult to find a player like this, and he has a lot of qualities. I hope he comes [back] soon."
Pogba said he has been frustrated with injuries this season but is ready to make an even stronger comeback when football returns.