The Magpies came from a goal behind to defeat the League One high-flyers and arguably cause the shock of the round thanks to goals in the second half from Connor Hall and Lewis Baines.
In truth, the victory was just what the visitors deserved as they dominated proceedings after Posh had taken an early lead.
In the first half they hit the woodwork twice and even missed a penalty in the second half.
It looked like it was going to be a long day for the Magpies after they got off to the worst possible start in the second minute.
A Mark Beevers corner was half-cleared to Jack Taylor, who thumped the ball into the roof of the net on the volley.
Ten minutes later, Matty Urwin was called upon to acrobatically turn away Mo Eisa thunderbolt from 35 yards.
Although the League One side were having the better of the early exchanges, slowly but surely the visitors began to grow into the game.
They had their first real chance on 16 minutes when Ollie Shenton found himself with time and space in midfield and looked to pick out Hall.
The match-winning hero of the first-round win over Wigan Athletic was through on goal, but Shenton's pass carried too much pace and Posh No.1 Christy Pym rushed out to smother the ball.
Three minutes later, Boro's million-pound rated centre forward Siriki Dembele fizzed free-kick over the bar, while Andy Halls' speculative long-range effort was meat and drink for Pym.
Chorley striker Harry Cardwell was certainly making his physical presence felt up front and he almost equalised for his team in the 28th minute.
After holding the ball up well initially, the ball was then into him on the edge of area.
He had his back to goal but turned superbly before firing a cannonball of a shot which rattled the post.
Soon after Cardwell is in the thick of the action when he headed Elliot Newby's centre back across goal but unfortunately Hall could not get on the end of it.
The Magpies continued to push forward but they were almost caught out shortly before halt-time by a Posh counter attack.
The hosts had four against two, but when the ball was played wide to Eisa, his shot after cutting in was tame and was easily saved by Urwin.
With the fourth official indicating there would be a minute of stoppage time at the end of the first half, Posh survived another attempt on their goal, this time by Newby.
The tricky midfielder won the ball and went on a barnstorming run through the centre of the pitch. He then curled a brilliant shot past the stranded Pym but the ball struck the post.
The rebound fell to Cardwell but he sliced his shot wide.
The Magpies continued to force the issue after the break with Posh boss Darren Ferguson becoming increasingly agitated on the sidelines.
In the 54th minute, great interchange play between Shenton and Newby released Baines down the left. His centre was met by Cardwell but his effort was deflected behind.
From the resulting corner, Halls blasted a piledriver over the bar.
Six minutes later, the Magpies finally got the reward their play richly deserved with the equaliser.
Baines throw-in from the left was played back to him by Newby and the left wing-back played a superb through-ball into the path of Hall, who controlled the ball before firing home from an acute angle.
Posh looked shell shocked and worse was to come for the League One high-flyers as their National League North opponents took the lead three minutes later.
And the goal looked like it came straight from the training ground.
Newby fired a corner to the edge of the area where the late-arriving Halls headed the ball back across the goal.
It fell to Baines who controlled the ball before firing home from six-yards, his shot taking a slight deflection on its way past Pym.
With 14 minutes to go Chorley had a great chance to seal their place in the third round when they were awarded a penalty.
Cardwell was blatantly bundled over by Mark Beevers in the 76th minute.
The former Grimsby Town striker picked himself up to take the spot kick but his well struck effort was superbly saved by Pym.
The Magpies continued to push forward in the final 10 minutes but Urwin was then called upon in the last minute of stoppage time when he blocked Dembele's effort.
Peterborough: Christy Pym, Dan Butler (Niall Mason 64), Mark Beevers, Frankie Kent, Mo Elsa, Jack Taylor, Siriki Dembele, Ryan Broom (Idris Kanu 69), Reece Brown, Sammie Szmodics (Flynn Clarke 57), Frazer Blake-Tracy
Subs: Daniel Gyollai (GK), Ronnie Edwards, Louis Reed, Ethan Hamilton.
Chorley; Matt Urwin, Arlen Birch, Harvey Smith, Andy Halls, Scott Leather, Lewis Baines, Mike Calveley, Harry Cardwell (Lewis Reilly 93), Elliot Newby, Ollie Shenton (Adam Henley 93), Connor Hall (Will Tomlinson 86)
subs: Oliver Putnam, Tyler Garratt, Malakai McKenzie, Sewa Marah.