The Sky Blues took the lead thanks to a Jordy Hiwula goal four minutes before the interval.
Darren Pratley restored parity for the Addicks after 58 minutes, but Tom Bayliss won it for the hosts with a last gasp winner.
Lee Bowyer’s injury woes continued when Geaorge Lapslie suffered a cut to his head in a stoppage time challenge with Luke Thomas.
Lapslie – a late substitute – left the field with his head swathed in bandages. But Thomas came off worse, and had to be stretchered off.
It was a poor performance by Charlton, with
Coventry having much the better of the first-half. Thomas was particularly impressive and gave Chris Solly – playing on the left – a torrid time.
Karlan Grant replaced the ineffective Nicky Ajose at the start of the second-half, and Mark Marshall – on for Ben Reeves – was another early change.
The duo had an immediate impact, and Pratley’s headed goal came from a Marshall free-kick.
The Addicks looked disjointed, and a number of players were below par. Bowyer’s team could not be faulted for effort though, but their cause was not helped by a difficult pitch.
Influential striker,Lyle Taylor, did not have one of his better games, and was perhaps fortunate to receive no more than a yellow card for a rash challenge on Thomas.
Charlton have a tough looking fixture at Barnsley on Saturday. The players will spend most of the time recovering before the clash at Oakwell, and Bowyer will work on motivating them for the game, as injuries and fatigue from the busy festive schedule kick in.
Here are Bowyer’s post match comments:
“It takes its toll, we don’t have people to bring in and we’re down to bare bones. We’ve got kids on the bench, left, right and centre with just Mark Marshall as the only senior one. You could consider Karlan senior, but he’s still young himself.
“It’s hard. We’ve got to play again in three days’ time. Joe Aribo is a big loss. He’ll be out for a little while. We never pick up a week-long injury, they’re always longer term and Joe is looking no different.
“George Lapslie is looking like another concussion. He’s got a big cut on his head and it’s not looking good. I’d be amazed if he was fit for Saturday.To get to where we are, the lads have been unreal.
“We don’t have the luxury of what other teams have got. We’re all digging deep and it is tough, but we’ll put this behind us and go again against Barnsley.
“I know I’ll get a good reaction because I’ve got a great bunch of lads in there who are all fighting.
“And the one thing I can say is that they give me everything until the end – they always do.
“We’ll patch the squad together and whoever steps out there, I know they will give 100 per cent. That’s a given. They know that that’s what I expect and that’s what I want and they give it, to be fair.
“It was a scrappy game on a bad pitch,” he said.
“It just wasn’t happening for us today. I tried to change it at half-time and played two wingers, hoping maybe they could make things happen, but it just wasn’t our day today.
“We just conceded two poor goals and left with nothing. A draw would have been a fair result.
“We’re all disappointed, it was a big opportunity to close the gap again, but it wasn’t meant to be and there’s still a long, long way to go.”
Charlton: Steer; Dijksteel, Bauer, Pearce, Sollly;Bielik (Lapslie 87), Pratley, Reeves (Marshall 57), Fosu; Taylor, Ajose (Grant 46).
Subs (not used): Phillips, Stevenson, Sarpong-Wiredu, Hackett-Fairchild.
Goal: Pratley 58.
Booked: Bauer 25 (foul ), Bielik 53 (foul ), Pearce 70 (foul ), Taylor 85 (foul ).
Coventry: Burge; Sterling, Hyam, Willis, Kelly, Mason (Brown 74); Thomas (Davies 90), Bayliss, Shipley (Clarke-Harris 64), Hiwula; Chaplin.
Subs (not used): Addai, Grimmer, Davies, Allassani, Westbrooke.
Goals: Hiwula 41, Bayliss 90.
Booked: Mason 50 (foul ).
Referee: Simon Hooper (Wiltshire).
Attendance: 13,013 (827 Charlton).