The 34-year-old goalkeeper has been restricted to just one appearance this season featuring in QPR's 4-0 FA Cup defeat to Everton earlier this month.
And, with a World Cup in his home country of Brazil looming this summer, Fernandes believes the former Inter Milan goalkeeper's future lies away from Loftus Road.
"I think so," Fernandes told Sky Sports News when asked if he thought Cesar was likely to leave the club in January. "It's a waste for someone with such immense talent not playing and I think he is one of the best goalkeepers in the world, so I'm sure someone will pick him up and let's see how that goes.
"We've gone with Rob (Green) because at the beginning of the season we thought Julio wouldn't be there. Rob has come in and done a fantastic job and I think he could be pushing for an England place - he's played really well.
"Just look at the last game (a 2-1 home victory over Huddersfield on Saturday). He kept us in the game till we came back and won. He's been superb."
Cagliari have been heavily linked with a move for the veteran stopper after the club's owner Massimo Cellino confirmed a meeting between the pair.
"I spoke to Julio Cesar who is not playing at QPR and wants to go to the World Cup," Cellino told Sardinian newspaper Unione Sarde.
"He told me that he knows the team and would return to Italy."
Cesar himself admits that he would consider a move to Sardinia in order to get more games under his belt.
"Me to Cagliari? Sardinia is well, there's always the sun, I'd like to go there," Cesar told tuttomercatoweb.com.
"Honestly, no offers have come in at the moment."
Fernandes said the club may add to the squad during the January transfer window but insisted the bulk of the transfer activity for the season has been concluded as QPR continue their quest for an instant return to the Premier League.
"We've done a remarkable job of moving on a lot and bringing in a great lot of players the squad is fantastic the spirit is great," he said.
"We would like to strengthen it a little bit here and there but most of the work has been done we wouldn't be second in the league with 52 points if we had lots of problems.
"But we've got to build on that and credit to Harry and the management team for putting in the work and bouncing back when everyone wrote us off and said we were the next club to go into ruin.
"We've come back smiling and looking good so the project is alive and we keep our fingers crossed that we make it to the promised land of the Premier League."