Albie Morgan’s 21st minute goal has given Charlton a 1-0 half-time lead over the Blues at Portman Road.
Liam Gibbs and David Cornell were handed their league debuts as manager Paul Lambert made four changes from the team which lost 3-0 at home to Hull City on Tuesday.
Gibbs, 17, came into the midfield three with Andre Dozzell, who was back after his three-match ban and Brett McGavin.
Bury St Edmunds-based academy product Gibbs, who had previously made two starts and one sub appearance in the EFL Trophy, started in a role ahead of the deeper Dozzell with McGavin completing one of the youngest midfields the Blues have ever fielded in a league game.
Emyr Huws is missing from the squad, presumably having joined Jon Nolan, Teddy Bishop, Flynn Downes, Cole Skuse and Tristan Nydam on a long midfield injured list.
Cornell took over in goal from Tomas Holy, who dropped to the bench. The Welshman had previously made five starts in cup games for the Blues since his summer move from Northampton.
At the centre of the defence, Toto Nsiala returned to the right of Luke Woolfenden with Mark McGuinness among the subs. Skipper Luke Chambers and Stephen Ward continued as the full-backs.
Up front, Keanan Bennetts was on the left and Alan Judge the right with James Norwood again the central striker.
For Charlton, manager Lee Bowyer, a former Blues midfielder, brought Chuks Aneke, Albie Morgan and ex-Blues loanee Jonny Williams into his XI for Omar Bogle, Alex Gilbey and Marcus Maddison, who were among the subs.
The Addicks were again forced to field a makeshift centre-half pairing of right-back Chris Gunter and midfielder Darren Pratley.
Prior to kick-off there was a minute’s applause in memory of football legend Diego Maradona, who died earlier in the week.
The game started scruffily but in the fifth minute McGavin won the ball midway inside the Charlton half and fed Bennetts, who took it on and hit a shot from the edge of the box which struck and Addicks defender. On the arm, according to Bennetts, but referee Craig Hicks showed no interest.
On 13 Judge found Chambers in space on the right. The Blues captain cut in and hit a shot with the outside of his boot which caught a defender on its way wide. From the resultant corner on the left, Nsiala rose highest but nodded beyond the far post.
A minute later, with Town looking the more dangerous side, Bennetts appeared to try to catch Addicks keeper Ben Amos unawares with a shot from wide on the left when a cross looked the more obvious option.
As the game approached the quarter-hour mark, the Blues came close to going in front when Dozzell played a ball through for Norwood, who held off Gunter but a heavy touch took it away from him and the striker was unable to avoid hooking his effort at goal from eight yards over the bar as well as Amos.
Two minutes later, Charlton felt they should have been awarded a penalty when Aneke’s flick sent Williams in on goal but Nsiala somehow got back to outmuscle the Welsh international and stab away and Cornell saved down to his right. A spot-kick would have been harsh but as Town know to their cost that penalties can be awarded in such situations.
The Addicks were starting to look more threatening and on 20 Aneke shot well over from a tight angle on the right.
And the South Londoners only had to wait another minute to go in front. Aneke won the ball from Woolfenden as he sought to play out on the edge of the area to the left and fed Andrew Shinnie. The Scot took it into the area before his low ball deflected off a Town defender to Morgan and the 20-year-old fired his first league goal for the Addicks past Cornell from 12 yards. Once again, Town’s defending had contributed much to an opposition goal.
In the 28th minute the Blues wasted a free-kick in a promising position not far outside the box. Dozzell played it wide to Judge on the left but the Irishman’s cross looped beyond Nsiala at the far post and out for a goal-kick.
Town lost striker Norwood to what looked to be another hamstring injury in the 35th minute. Aaron Drinan replaced the former Tranmere man a minute later, while Ward was receiving treatment for a knock of his own. Norwood’s exit was the third time in three games the Blues had lost a player to injury in the first half.
Drinan was making his first appearance since the opening day of the league season when he suffered a thigh injury in the 2-0 victory over Wigan.
The visitors had keeper Amos to thank for maintaining their 1-0 lead in the 38th minute, the keeper flying away to his right to palm Judge’s flicked header from Dozzell’s free-kick on the right past his post.
A minute later, Drinan won the ball on the byline from the hesitant Pratley and cut it back to Judge, whose shot was somehow deflected over by Ian Maatsen. As has been the case too often of late, Town’s corner came to nothing.
In the 43rd minute Judge was shown the game’s first yellow card for a foul on Shinnie as Charlton broke.
In the final scheduled minute of the half, Paul Smyth got away behind Nsiala but threw himself to the ground just outside the area as the defender looked to get back in front of him. Referee Hicks was unimpressed with his dive but showed no card.
As half-time approached, most of the game was being played in the visitors’ half of the field but with Blues passes going astray at vital moments.
Again Town were left rueing having not taken chances at one end while being the architects of their own downfall at the other with there having been little between the sides during what had been a scruffy half overall.
Norwood will feel he should have taken his chance, while Judge’s header was kept out by an excellent Amos save, although the Irishman may believe he should have scored his other opportunity after Drinan had done well to win the ball back on the byline.
Keeper Cornell had had a relatively quiet half but the Blues still found themselves behind at the break from another very preventable goal.
Town: Cornell, Chambers (c), Woolfenden, Nsiala, Ward, Dozzell, McGavin, Gibbs, Bennetts, Judge, Norwood (Drinan 36). Subs: Holy, McGuinness, Kenlock, Lankester, Hawkins, Jackson.
Charlton: Amos, Gunter, Williams, Aneke, Shinnie, Pratley (c), Matthews, Morgan, Maatsen, Watson, Smyth. Subs: Maynard-Brewer, Purrington, Pearce, Gilbey, Bogle, Maddison. Referee: Craig Hicks (Surrey).