Darren Bent came off the bench to help fire Charlton into the third round of the Carling Cup.
The visitors took a shock lead five minutes before the break when Thomas Butler picked out Jon Daly to drill a low shot into the bottom corner.
Charlton soon equalised when Lloyd Sam was felled in the box and Jonatan Johansson scored from the spot.
Bent headed the Addicks ahead and fellow substitute Jay Bothroyd drilled in a fine strike to seal their passage.
Charlton: Myhre, Young, Spector, Sorondo, Hreidarsson, Sam, Smertin (Murphy 68), Holland, Thomas, Johansson (Bothroyd 75), Bartlett (Bent 45).
Subs Not Used: Andersen, Fortune.
Booked: Bothroyd, Spector.
Goals: Johansson 43 pen, Bent 73, Bothroyd 80.
Hartlepool: Konstantopoulos, Darren Williams, Nelson, Collins, Humphreys, Istead (Llewellyn 57), Sweeney, Tinkler (Turnbull 81), Butler, Proctor, Daly (Foley 72).
Subs Not Used: Provett, Jones.
Booked: Humphreys.
Goals: Daly 40.
Att: 10,328
Ref: G Hegley (Hertfordshire).