Fees have been agreed for both players, and Tottenham midfielder Sandro is undergoing a medical ahead of the 11pm deadline.
But Rangers have so far been unable to agree personal terms with Liverpool forward Borini, who has already rejected a move to Sunderland this summer.
Speaking to Sky Sports News HQ outside Loftus Road, Fernandes said: "I'm not confident Borini will happen.
"I think players' expectations, agents' expectations...sometimes people have to be a bit realistic and we're not going to do anything silly. I'm not optimistic."
Sandro, at least, is on course for a reunion with Harry Redknapp, who signed the Brazilian during his time at White Hart Lane.
Redknapp said: "Sandro was a fantastic player for me. He’s having a medical and I think everything is agreed with Tottenham so that one should happen."
A deal for Toronto's Jermain Defoe is not dead in the water, either, although Fernandes says it may not happen until January given the MLS season is still ongoing.
Niko Kranjcar, who played under Redknapp at Portsmouth and Spurs and was on loan at QPR last season, is also in west London to discuss a move.
And Redknapp insisted on Monday evening there was still a chance a deal for Lokomotiv Moscow's Lassana Diarra could be revived.
That transfer appeared done at the weekend only to collapse early on deadline day, but Redknapp told Gary Cotterill: "I think that one is still going on so we’ll see."