Having gone in front on two occasions through on loan striker Dave Kitson, Peterborough pulled themselves level twice through George Boyd and Shaun Batt.
There should, however, have been a further chance for Middlesbrough to seal the first three points of the Strachan era, but the match official, Phillips, turned a blind eye.
Moments after Batt had struck an unstoppable 76th minute leveller with a stunning volley on the turn, Boro responded by heading down the other end in search of another.
But when it looked certain they would be awarded a penalty when Aaron McLean appeared to bring down Sean St Ledger in the area, Phillips waved play on, much to Boro's frustration.
A failure to hold on to their one goal lead which they held twice - means that Middlesbrough have lost further ground on the Championship's top two, with Newcastle and West Brom both winning.
Now Middlesbrough, despite Kitson's double, are 13 points adrift of their North-East rivals and 11 behind the second placed Baggies.
PETERBOROUGH (4-4-2): Lewis; Zakuani (Lee 60, 5), Geohaghon, Bennett, Griffiths; Rowe (Batt (67, 5), Diagouraga, Frecklington, Boyd; McLean, Mackail-Smith. Subs: Coutts, Keates, McKeown, Green, Simpson.
MIDDLESBROUGH (4-4-2): Jones; McMahon, St Ledger, Wheater, Pogatetz; Yeates (Hoyte 75), Osbourne, Arca, Johnson; Kitson, Lita. Subs (not used): Taylor, Riggott, Digard, Emnes, Bent, Coyne.