A second-half double from Graham Kavanagh condemned Charlton to their second defeat of the season.
The veteran midfielder's goals, both long-range strikes, came after two controversial penalty incidents.
Ian Harte converted the rebound for Carlisle after his 41st-minute penalty, awarded for holding, had been saved.
But Charlton levelled moments later when Deon Burton was brought down on the edge of the box - a penalty was given, which Burton duly converted.
Charlton manager Phil Parkinson told BBC London 94.9:
"We've lost the game to two special goals from Graham Kavanagh.
"The first one certainly gave the Carlisle team and supporters a lift and they responded to it by raising their game by 15-20 per cent and we didn't raise our game in response to that.
"In patches we played ok, but, at times in the second half, we gave the ball away too cheaply and caused ourselves problems."
90:00+5:05 The referee blows his whistle to end the game.
90:00+0:14 The ball is delivered by Lloyd Sam, Richard Keogh makes a clearance.
89:21 David Mooney is flagged offside by the assistant referee. Free kick taken by Leonard Pidgeley.
87:21 Substitution Marc Bridge-Wilkinson replaces Vincent Pericard.
85:01 Shot from a long way out by Deon Burton goes wide of the left-hand upright.
84:27 The ball is crossed by Matthew Robson, Christian Dailly manages to make a clearance.
82:36 Assist by Scott Dobie.
82:36 GOAL - Graham Kavanagh:Carlisle 3 - 1 Charlton Graham Kavanagh grabs a goal from long distance to the top right corner of the goal. Carlisle 3-1 Charlton.
82:11 Lloyd Sam sends in a cross.
81:40 Foul by Scott Dobie on Therry Racon, free kick awarded. Carl Ikeme takes the free kick.
81:10 Substitution Joe Anyinsah joins the action as a substitute, replacing Kevan Hurst.
80:16 A cross is delivered by Nicky Bailey.
79:18 The assistant referee signals for offside against Vincent Pericard. Indirect free kick taken by Carl Ikeme.
78:08 Foul by Tom Taiwo on David Mooney, free kick awarded. Jonjo Shelvey shoots direct from the free kick, save made by Leonard Pidgeley.
77:27 Grant Basey delivers the ball, Headed effort from inside the area by David Mooney misses to the right of the goal.
75:54 Corner from right by-line taken by Grant Basey.
75:27 Corner taken by Nicky Bailey, Scott Dobie makes a clearance.
75:08 Shot by Therry Racon from 18 yards. Leonard Pidgeley makes a save.
74:32 Matthew Robson takes a shot. Therry Racon gets a block in.
73:22 Free kick awarded for a foul by Christian Dailly on Vincent Pericard. Ian Harte crosses the ball in from the free kick, clearance by Sam Sodje.
72:46 Centre by Richard Keogh.
70:40 Substitution Elliot Omozusi leaves the field to be replaced by Grant Basey.
70:40 Substitution David Mooney comes on in place of Izale McLeod.
70:40 Substitution Jonjo Shelvey on for Jose Vitor Semedo.
70:23 Shot from outside the area by Tom Taiwo misses to the left of the target.
67:30 Outswinging corner taken from the right by-line by Kevan Hurst, save by Carl Ikeme.
64:57 The assistant referee signals for offside against Deon Burton. Leonard Pidgeley takes the indirect free kick.
64:21 The offside flag is raised against Vincent Pericard. Carl Ikeme restarts play with the free kick.
62:29 The assist for the goal came from Tom Taiwo.
62:29 GOAL - Graham Kavanagh:Carlisle 2 - 1 Charlton Graham Kavanagh finds the net with a brilliant goal from 35 yards to to the bottom left corner of the goal. Carlisle 2-1 Charlton.
61:56 Matthew Robson delivers the ball, Sam Sodje makes a clearance.
60:55 Matthew Robson crosses the ball, Vincent Pericard takes a shot. Save by Carl Ikeme.
60:13 A cross is delivered by Richard Keogh, Headed effort from deep inside the penalty area by Vincent Pericard goes harmlessly over the crossbar.
60:02 The ball is crossed by Scott Dobie, clearance made by Sam Sodje.
56:37 Free kick awarded for a foul by Therry Racon on Matthew Robson. Free kick taken by Leonard Pidgeley.
56:08 Corner taken by Kevan Hurst from the right by-line, Elliot Omozusi makes a clearance.
54:52 Jose Vitor Semedo concedes a free kick for a foul on Vincent Pericard. Shot comes in from Ian Harte from the free kick, blocked by Nicky Bailey.
54:22 The assistant referee signals for offside against Kelly Youga. Leonard Pidgeley restarts play with the free kick.
51:35 Shot by Kelly Youga from 30 yards. Comfortable save by Leonard Pidgeley.
51:21 The ball is delivered by Nicky Bailey, Danny Livesey manages to make a clearance.
48:33 The ball is sent over by Nicky Bailey, Headed effort on goal by Sam Sodje from inside the penalty box misses to the right of the target.
48:33 Booking The referee shows Scott Dobie a yellow card.
48:19 Scott Dobie gives away a free kick for an unfair challenge on Jose Vitor Semedo.
47:54 Shot from 12 yards from Lloyd Sam. Danny Livesey gets a block in.
47:24 Free kick awarded for an unfair challenge on Jose Vitor Semedo by Matthew Robson. Direct free kick taken by Carl Ikeme.
47:01 Deon Burton is penalised for a handball. Leonard Pidgeley takes the direct free kick.
46:15 Outswinging corner taken right-footed by Nicky Bailey from the right by-line.
45:01 The referee gets the second half started.
Half Time
45:00+4:04 It is the end of the first-half.
45:00+3:15 Effort on goal by Deon Burton from just inside the area clears the crossbar.
45:00+1:50 Corner taken by Matthew Robson.
45:00+1:37 The ball is delivered by Richard Keogh, clearance by Sam Sodje.
44:17 Penalty awarded for a foul by Graham Kavanagh on Deon Burton.
43:50 Foul by Graham Kavanagh on Lloyd Sam, free kick awarded. Free kick taken by Elliot Omozusi.
40:30 GOAL - Ian Harte:Carlisle 1 - 0 Charlton Ian Harte grabs a goal from close range to the bottom right corner of the goal. Carlisle 1-0 Charlton.
38:43 A save by Carl Ikeme from penalty by Ian Harte. Carlisle 0-0 Charlton.
38:43 Outswinging corner taken right-footed by Kevan Hurst, Richard Keogh fouled by Deon Burton, the ref awards a Penalty.
37:21 Izale McLeod challenges Richard Keogh unfairly and gives away a free kick. Free kick crossed by Ian Harte, Nicky Bailey manages to make a clearance.
36:00 Direct effort from the free kick comes in from Ian Harte.
36:00 Booking Booking for Christian Dailly for unsporting behaviour.
35:41 Foul by Christian Dailly on Scott Dobie, free kick awarded.
33:27 Unfair challenge on Therry Racon by Ian Harte results in a free kick. Free kick taken by Carl Ikeme.
32:35 Free kick awarded for an unfair challenge on Scott Dobie by Elliot Omozusi. Free kick crossed left-footed by Ian Harte, Christian Dailly makes a clearance.
31:52 Graham Kavanagh takes a shot. Carl Ikeme makes a comfortable save.
31:29 Unfair challenge on Kevan Hurst by Jose Vitor Semedo results in a free kick. Richard Keogh takes the direct free kick.
30:43 Scott Dobie takes a shot. Save made by Carl Ikeme.
29:40 Shot on goal by Nicky Bailey from just inside the area clears the crossbar.
29:00 Matthew Robson produces a left-footed shot from a long way out which goes wide right of the goal.
Correction - 28:39 Matthew Robson takes the chance to get an effort at goal. Blocked by Elliot Omozusi.
28:39 Matthew Robson takes a shot. Elliot Omozusi gets a block in.
28:02 A cross is delivered by Izale McLeod, clearance by Danny Livesey.
27:09 Nicky Bailey fouled by Kevan Hurst, the ref awards a free kick. Free kick taken by Carl Ikeme.
25:48 The ball is delivered by Nicky Bailey, clearance made by Evan Horwood.
23:54 Matthew Robson gives away a free kick for an unfair challenge on Izale McLeod. The free kick is delivered right-footed by Nicky Bailey from left wing, comfortable save by Leonard Pidgeley.
23:09 Unfair challenge on Vincent Pericard by Jose Vitor Semedo results in a free kick. Free kick crossed by Graham Kavanagh, clearance made by Nicky Bailey.
21:26 Shot from long range by Therry Racon misses to the right of the goal.
20:10 Foul by Tom Taiwo on Izale McLeod, free kick awarded. Shot comes in from Nicky Bailey from the free kick, blocked by Scott Dobie.
18:51 Corner taken by Matthew Robson, Sam Sodje manages to make a clearance.
17:58 Unfair challenge on Graham Kavanagh by Elliot Omozusi results in a free kick. Free kick crossed left-footed by Ian Harte, Sam Sodje manages to make a clearance.
17:46 Kevan Hurst sends in a cross, Sam Sodje makes a clearance.
17:05 Nicky Bailey sends in a cross.
15:12 Deon Burton is penalised for a handball. Free kick taken by Leonard Pidgeley.
13:04 Foul by Scott Dobie on Kelly Youga, free kick awarded. Christian Dailly restarts play with the free kick.
10:49 Graham Kavanagh has an effort at goal from outside the penalty area which goes wide right of the goal.
10:36 The ball is swung over by Richard Keogh, Christian Dailly makes a clearance.
9:18 Foul by Kelly Youga on Vincent Pericard, free kick awarded. Leonard Pidgeley restarts play with the free kick.
8:32 The ball is sent over by Lloyd Sam, clearance by Richard Keogh.
7:05 The ball is sent over by Lloyd Sam, Tom Taiwo manages to make a clearance.
5:31 Lloyd Sam crosses the ball, comfortable save by Leonard Pidgeley.
1:28 A cross is delivered by Lloyd Sam, comfortable save by Leonard Pidgeley.
1:08 The ball is crossed by Lloyd Sam, Richard Keogh makes a clearance.
0:00 The match has kicked off.
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