The Addicks were facing relegation to the third tier on a points-per-game basis had the second tier been unable to resume due to the coronavirus pandemic.
But Bowyer's men hit the ground running after the 15-week break, with captain Jason Pearce's bundled first-half effort enough to see off lacklustre Hull 1-0 and leapfrog them in the standings.
Former Whites favourite Bowyer has already stated how he would love to see Leeds promoted to the Premier League and both the Whites and Addicks will hope they have achieved their objectives by the time the two teams meet at Elland Road on the final day of the regular season on Wednesday, July 22.
"The good thing is that if you can get off to a winning start like now, we're out of the bottom three," the Charlton manager said. "Now it's in our hands, you know?
"I believe in the players and I've said that all the way along. Once we get out, now it's down to us.
"Now we've got a week to prepare for QPR. It's going to be another tough game but I've just said to them it's another game that we can win if we do the right things.
"It's a good start but it's not over yet. We've got to keep fighting for every point and the players done that today. I'm really proud of them.
"I think it was well deserved.
"I think from the first whistle we were at it.
"We looked sharp. This week building up to it, I said to the players that they've had a good week and they're ready to go and they showed that.
"To get the goal quite early on was nice. I think we settled down after that and we got into some very good areas.
"I thought that on another day we could have maybe scored another two or three goal if the quality was a little bit better in the final third, picking out the right pass.
"But, yeah, overall clean sheet as well, so very, very pleased."