Injury prevented Boro skipper Gary O'Neil from making the 300th appearance of his career.
Barry Robson took over the captain's armband and celebrated with an early goal.
When Jonathan Franks crossed from the left, Robson gave Joe Lewis no chance for his first Middlesbrough goal following his move from Celtic in the January transfer window.
Middlesbrough piled on pressure in a determined bid to increase the scoreline.
Scott McDonald tried a long-range shot that went sailing over the bar while Lee Miller also shot wide.
Boro dominated possession without making it count. They were probing on both wings without troubling Lewis after the opening goal.
Peterborough were lacking confidence and had little to offer, although Lee Frecklington had a shot charged down.
Lewis made a brilliant near-post save from Willo Flood.
There was a lack of thrills and a subdued atmosphere and the game needed another goal to liven up the crowd.
The crowd encouraged Franks to have a go and Lewis was forced into a good save.
In injury time Peterborough came close to snatching an equaliser when Danny Coyne was forced to pull off a brilliant one-handed save from a Frecklington shot.
After the break Peterborough showed more self-belief and determination. For the first time they looked as though they could pull the game round and Middlesbrough fans wondered whether their team could suffer from making the most of their first half possession.
In stoppage time Middlesbrough central defender David Wheater rescued his side when he cleared off the line from Josh Simpson.
Middlesbrough extended their unbeaten run to six matches - an impressive record bearing in mind they were in freefall earlier in the season with the fear that they could be locked in a relegation battle.