We deserved Wigan Athletic victory - Charlton boss
Jake Forster-Caskey scored the only goal midway through the second period, with a 30-yard free-kick that deceived Latics goalkeeper Jamie Jones.
But the visitors will point to a disallowed goal from Joe Garner, as well as two huge penalty shouts, as proof they warranted something from an entertaining encounter.
“It was a tough game between two solid teams, and we had to be at it from the first whistle to the last," assessed Bowyer.
“We started really well, on the front foot for the first 20 minutes.
"When you are on the front foot like that you need to be more clinical.
"And we will be once we start working with this group more.
“Overall, it’s probably fair that we won that game.
"The most pleasing thing for me is that they all dug deep at the end to hold onto the three points.
"You’ve got to do that and put your bodies on the line.”
Bowyer handed debuts to four new signings, with Latics legend Ben Watson also making only his second start in the league.
“The new boys did very well, especially when you consider the fact that two of them only signed Friday morning, and it was a good team performance," added the Addicks boss.
"There were a lot of positives, and not too many negatives.
“When we have so many new signings in the side, I try not to complicate things and tell them too much. But there are things we want to work on and improve.
“We’ve got a good group here, and we just need to tidy up a few things.”