Ricky Holmes, Ademola Lookman and Josh Magennis goals were enough to see off the Sky Blues, who remain bottom of League One.
Charlton and Coventry fans marched to the ground together in a pre-match protest against their respective owners Roland Duchatelet and Sisu.
As soon as the game kicked off, there was a six-minute stoppage in play after home and away supporters threw thousands of toy pigs onto the pitch.
Both teams hit the woodwork in the first half but it was Charlton who took the lead when Fredrik Ulvestad's lobbed pass found Holmes, who poked the ball home in the 32nd minute.
Charlton goalkeeper Declan Rudd made a sublime double save early in the second half when he stopped Andre Wright's effort and then got back up to push Chris McCann's header away from goal.
The game was over with 12 minutes to go after Magennis unselfishly squared the ball to Lookman, who fired past Lee Burge.
The Northern Ireland international grabbed himself a goal in the 88th minute when he chipped the ball over the helpless Coventry stopper.
The result meant Charlton won their first league game since August 20.