O'Neil is missing with a groin problem, paving the way for Irishman Mark Yeates to come in and fill the hole on the right flank, with Julio Arca slotting inside.
In the absence of the suspended Rhys Williams, meanwhile, Tony McMahon is given his first opportunity under Gordon Strachan at right-back.
On loan striker Marcus Bent has passed a late fitness test to start, meaning teenager forward Luke Williams missed out on a place on the bench.
PETERBOROUGH (4-4-2): Lewis; Rowe, Zakuani, Geohaghon, Griffiths; Bennett, Diagouraga, Frecklington, Boyd; McLean, Mackail-Smith. Subs: Lee, Coutts, Keates, McKeown, Batt, Green, Simpson.
MIDDLESBROUGH (4-4-2): Jones; McMahon, St Ledger, Wheater, Pogatetz; Yeates, Osbourne, Arca, Johnson; Kitson, Lita. Subs: Hoyte, Taylor, Riggott, Digard, Emnes, Bent, Coyne.