With a trip to Stoke to come next Saturday and games against fellow strugglers Luton and Huddersfield to follow in a packed February, Bowyer was pleased his side maintained their four-point cushion over the bottom three with a 2-1 home win.
He said: "It was an important win, especially when it comes against one of the teams around you in the table.
"The performance could have been better and we were sloppy in the middle of the park but I never question the fighting spirit of my players.
"I thought we were comfortable in the first half and we kept them really quiet, even though Dillon Phillips had to make a brilliant save.
"But Barnsley changed things at half-time and matched us up. They did put us under a bit of pressure and we rode our luck towards the end.
"It is amazing what a win does to lift the crowd, but they have been like that this season when we've been losing as well.
"They know that they play a massive part here and, as a footballer, it does give you a lift when you see the place near on full.
"It is amazing how many times the board goes up from the fourth official with six or seven minutes on it when we are leading, but then it only says three or four when we are in a losing position.
"We have given up leads in some games but today showed that we are learning to hold on. Now we have to get ready for Stoke next week.
"I hope I'll sleep like a baby tonight. I only got home at one o'clock because of the transfer deadline last night.
Bowyer praised the determination of on-loan Aston Villa striker Andre Green to play in spite of the death of his grandfather earlier in the week. Green scored Charlton's second goal, after Lyle Taylor had given them an early lead.
The boss explained: "Andre had some bad news earlier in week and did well to even turn out today. He has only been here five minutes and he's already scored two goals."
Barnsley manager Gerhard Struber was furious with his side's defending from set pieces, which cost his side both goals.
Struber said: "It is always the same mistakes, the same as last week at Portsmouth. Set plays were the difference again today and that is why we have lost.
"The problem is that set plays are now a very important part of football and you have to be able to defend them.
"In every other phase of our play, how we build up the play and the way we create chances, we are ready for the Championship, but it is clear that we are not ready for the Championship from set plays. This is the reality. We don't stay in our structure at them.
"We spent a lot of time on set pieces this week but at the end we made no progress in them.
"It was a big game for us, a six-point game. That was very clear to us before the game. And we created lots of chances with our play. I am very frustrated.
"We hit the post and crossbar three times from chances that we created, so that makes it even more disappointing.
"When I see what we can do, what we create, we had good pressure on Charlton in the second half, good rotation of the ball and we hit the crossbar three times, that makes me all the more disappointed.
"This defeat was not necessary and we were a bit unlucky in the end, but I have no words to describe my feelings now.
"We brought good players into the club in the transfer window. We have to work hard now – and I believe that we can stay in the league."