Garry Flitcroft's side lead for over an hour at Victory Park as Darren Stephenson's 23rd minute shot deflected in off Hugo Fernandez, but late goals from Patrick Antelmi and Fernandez saw the young Rovers triumph.
It was the home side who started the brighter of the two, Josh Hine seeing a goal disallowed whilst Darren Stephenson was denied by a save from Matty Urwin in the early exchanges.
Then a 16th minute Chorley corner saw Andy Teague head goalwards but Hugo Fernandez headed off his own line.
Rovers struggled to create in the opening exchanges but John O'Sullivan should have perhaps done better on 19 minutes. But after getting past three defenders he put his effort wide of goal.
Rovers were to regret that missed chance as the home side took a 23rd minute lead. Darren Stephenson with a ball into the area and it deflected off Spaniard Fernandez and past an unsighted Urwin into the back of the net.
Boosted by the goal the Magpies went in search of more, Urwin saving well from Stephenson, whilst Jake Cottrell went close with a header.
The only other chance of note in the first half for Rovers fell to trialist Patrick Antelmi, but when well-placed he fired straight at Sam Ashton in the Chorley goal.
The second half started with Chorley continuing to force the pace, Hine being denied by Urwin, the Rovers goalkeeper then saving well from Carlos Roca.
However just when it seemed as if Chorley would ease to victory, Antelmi struck with four minutes from time. Taking advantage of some hesitant defending to fire home.
Rocked by the equaliser, Chorley then conceded a later winner as Hugo Fernandez scored for Rovers with a minute left on the clock.
The young midfielder showing good composure to finish well after space opened up in the area.
It was the last action of the match with Rovers running out 2-1 winners.
Eric Kinder's side are back in action this Saturday when they take on Northwich Victoria at Valley Road, Flixton.