The Addicks created the better chances throughout but some resolute defending by the visitors side kept Charlton out in the first period.
Darren Ambrose hit the outside of the post with a close-range header after 17 minutes.
The ex-Ipswich man also rattled the Carlisle woodwork again on the half-hour mark with a 25-yard effort that crashed back off Anthony Williams' crossbar.
The best opportunity for the Cumbrians early on was sandwiched between the Ambrose show.
Chris Lumsdon's goalbound shot deflected behind off Radostin Kishishev before Carlisle centre-half Peter Murphy headed the resultant corner inches over the top.
The visitors came out pumped up after the break and were the better side before the Addicks found the breakthrough goal.
Carlisle's impressive Murphy curled a wicked left-foot shot against the Charlton crossbar from distance on 55 minutes.
Shortly afterwards though Darren Bent showed his predatory instincts in front of goal when he toe-poked home at the far-post after Williams had made a sharp save from Dennis Rommedahl's 12-yard effort.
Taking the lead visibly gave the Addicks - who have lost four of their five Premier League games this season under new boss Iain Dowie - confidence to start playing the ball around and hold on to possession as they looked to make the Cumbrians work hard.
The pacey Darren Bent fired over after being sent clear by Ambrose on 63 minutes as the home side controlled the game and saw out the victory.