The Addicks were the first club in London to welcome back 2,000 supporters under the country's new coronavirus restrictions, but the visitors ruined the party at The Valley, with Scott Fraser's late goal earning the Dons a deserved 1-0 win.
Supporters were socially distanced, spaced across three stands and told to wear masks at all times, except when eating or drinking.
On the eve of their return, Bowyer urged supporters to make "as much noise as humanly possible", but afterwards said he was surprised by the returning fans, many of whom have not been to a game since March.
“We’ve been wanting them to come back from day one and they’ve been kept away," Bowyer said. "Even though it was 2,000 I expected non-stop singing, supporting the players and pushing them. But it wasn’t like that.
“It was very, very quiet apart from some negative shouting – and I didn’t expect that tonight.
“Listen, the players didn’t really do too much to get people on their feet, but sometimes they need a bit of help, and that’s what our fans are great at.
“It wasn’t what I expected, because we don’t stop singing normally. And there wasn’t much singing at all, from start to finish, tonight.”
Bowyer added: “I’m pleased to see them back in. I would have liked it to have been a bit more positive from the fans.
“They’ve been away so long, I’d rather they get behind the team and try and get them going. Because they played a hard game on Saturday against Ipswich and when we play at home we need those fans to be positive and pick the lads up when it’s not going so well.
“That’s what I’d rather have happened tonight. But I’m glad they are back in, because we’ve missed them. I just wish they were a little more vocal tonight in helping the lads."
Before the match, Bowyer told Standard Sport that playing behind closed doors had killed home advantage, but Wednesday night's defeat was only the Addicks’ second at The Valley in League One this season, with the other coming to Doncaster in front of 1,000 fans at a pilot event in September.
Asked if the pressure may have affected his players, Bowyer said: “I’ve just said to them in there, if you can’t play in front of 2,000 then stop the game now. Because this stadium will be full again – 2,000 is not a big amount of people, so you shouldn’t get nervous and doing the wrong thing or hiding from the ball. None of them did that.
“I don’t believe [the crowd] made a difference."
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