The defender, who is expected to leave the Riverside in this month's transfer window, has been excluded from Tony Mowbray.
Both Bolton and Stoke are understood to have inquired about Wheater's situation this week, and by not playing today, the centre-half will ensure he is not cup-tied for future rounds of the competition.
Boro are also without injured trio Jason Steele, Barry Robson and Kevin Thomson as they attempt to avoid a shock at the Pirelli Stadium.
Danny Coyne replaces Steele between the sticks, with Seb Hines coming in for Wheater at centre-half.
Jason Hoyte is expected to start on the right of midfield, while Kris Boyd gets a rare start in attack alongside Leroy Lita.
BURTON (4-4-2): Legzdins; Austin, Stanton, Moore, Malone; McGrath, Bolder, Penn, Webster; Maghoma, Harrad.
Subs: Poole (gk), Boertien, James, Phillips, Pearson, Young, Hughes.
MIDDLESBROUGH (4-4-2): Coyne; McMahon, Bates, Hines, Bennett; Hoyte, O'Neil, Bailey, Arca; Boyd, Lita.
Subs: Ripley (gk), Kink, Halliday, L Williams, Franks, Smallwood, Park.
Source: Northern Echo
Source: Northern Echo