Fernandes, who has nine goals and 14 assists for United this season, missed their 3-2 win over Tottenham Hotspur on the weekend, along with team mates Luke Shaw and Scott McTominay.
While giving an update on the status of the trio, Rangnick said Bruno's absence was caused by a positive Covid-19 test.
"With Scotty, I hope (he is fit) but he had some muscular problems with his calf," Rangnick said. "That's why we decided not to play him (against Spurs), because Scotty ... is only valuable if he can perform with 100% of his physical capacity.
"Luke hopefully will be back in training Monday and Bruno we will have to wait and see until Tuesday. This will probably be a last-minute race with him - due to Covid-19.
"We have to be careful with Covid-19 tests. David (de Gea) was the same. David yesterday was out, he was not supposed to play but then it turned out that his first fast test was false."
Anthony Elanga salvaged a 1-1 draw for United in the first leg against Atletico in February with a late equaliser, leaving the tie finely poised ahead of the return leg.
(Reporting by Aadi Nair in Bengaluru; Editing by Tom Hogue)
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