Rae broke two bones in his hand during Monday's astonishing 4-4 draw at Peterborough in which the Bluebirds threw away a 4-0 half-time lead.
His absence leaves manager Dave Jones short of options in central midfield with Stephen McPhail still sidelined and Riccy Scimeca having retired while Joe Ledley is constantly playing through the pain barrier as he battles his hip injury.
Rae's absence means Peter Whittingham, who has a slight thigh problem himself but should be okay, is likely to move into the middle to partner Ledley, with Kelvin Etuhu starting on the wing.
Striker Jay Bothroyd is also doubtful at Ashton Gate having sustained a swollen knee against Posh while full-back Mark Kennedy is facing a battle to be involved having tweaked a calf in training.
But Jones has received a boost with the news Kevin McNaughton should be fit having come off at half-time on Monday nursing a tight hamstring.
Bristol City manager Gary Johnson will have to reshuffle his defence.
Johnson will be without defenders Lewin Nyatanga, Jamie McCombe and James Wilson for the third-round tie at Ashton Gate.
Nyatanga is missing as he serves a one-match ban for his sending off in the 2-2 draw with Watford on Monday. McCombe is still out with several minor knocks, while James Wilson is also injured.
Johnson looked to strengthen his defence by recalling Christian Ribeiro from his loan spell at Stockport during the week.
But the Wales Under-21 international is likely to start from the bench, with Liam Fontaine set to line-up in defence alongside Bradley Orr, Louis Carey and Jamie McAllister.
City will also be without Evander Sno, who is still absent on compassionate grounds, while Lee Johnson a doubt through illness.