The Addicks are set to sell out their 36,000-plus allocation for Wembley as they take on Sunderland in the League One play-off final on Sunday.
Supporters have been protesting against controversial owner Roland Duchatelet for most of his five-year spell in SE7.
The Belgian, who is eager to sell up, has hired seven different managers, sold Charlton’s best players and accused fans of ‘wanting the club to fail’.
Despite the unrest, Bowyer, along with assistant and club legend Johnnie Jackson, have brought the feel-good factor back to the Valley since replacing Karl Robinson 15 months ago.
Speaking on Wednesday’s Alan Brazil Sports Breakfast, Bowyer told talkSPORT: “No one tipped us to be in the top six so to have a day out at Wembley, it’s a great achievement for our football club.
“At the start of the season, the big thing for me was to try to bring the fans and players together because everyone knows there was a lot of negativity around the football club before I came in.
“I wanted to bring them back together and make sure they were part of the journey that we were going to go on.
“I honestly did believe that we had a good chance [of promotion] this season and to make our home ground a bit of a fortress.
“When you’re playing and you’ve got good crowds behind you, all the fans want to see is the players giving 100 per cent and that was something I demand from my players.
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“The fans see that and then they come back and the place is erupting. The other night [against Doncaster], we filled the Valley for the first time in I don’t know how many years. It’s just been great from start to finish.”
Charlton are just one game away from ending their three-year exile from the Championship.
They face Sunderland in a repeat of the thrilling 1998 Division One play-off final, which the Addicks won on penalties.
Promotion would see Bowyer go head-to-head with former club Leeds next season.
“That would be interesting, but it’s one step at a time, we’re just delighted to be where we are at the moment,” he added.