Ishmael Miller sealed victory for promotion-chasing Boro in the npower Championship encounter at London Road by slamming in a 76th-minute winner, just three minutes after his introduction.
Boro had earlier seen Faris Haroun's early brace wiped out as Peterborough's on-loan striker Dwight Gayle struck twice.
Mowbray admitted he was fearing the worst after seeing his side throw away a two-goal lead, but Miller's low 20-yard strike, which caught out goalkeeper Bobby Olejnik, secured the points.
Mowbray said: "We came here to win, we would have been disappointed to draw and yet we could even have lost. It was all about the three points and we got them in the end.
"A fantastic goal brought Peterborough back into it and a sloppy one got them level, but I'm thankful our changes worked well."