Visitors Leverkusen went 2-0 in front when Stefan Kiessling was credited with the controversial goal during the second half, and a late reply from Sven Schipplock was only a consolation for Hoffenheim.
Hoffenheim lodged an appeal against Friday's result after television replays confirmed Kiessling's header entered the goal through the side-netting.
"There was no indication that it was not a regular goal," Brych, a FIFA referee, said at the Rhein-Neckar-Arena.
"I had a bit of doubt, but the reaction of the players was clear. There was nothing to suggest otherwise."
His comments, reported on Hoffenheim's website, reflected Leverkusen's players celebrating the goal and Hoffenheim's defenders looking away as if it was valid.
Kiessling initially appeared disappointed with the miss, then shocked that his team-mates congratulated him.
The referee's mistake could have consequences though, like an almost identical precedent in Bayern Munich's 2-1 win over Nurnberg in 1994.
In that game, Bayern's Thomas Helmer dragged an attempt wide of the goal, but the linesman on the opposite side of the field claimed it had gone in and the referee agreed. That game was replayed, with Bayern running out 5-0 winners.
Hoffenheim coach Markis Gisdol said: "It's definitely bitter for us and something like this has already happened once, and that game was replayed so I think we're going to see this game again.
"Anything else would be a joke. You can't replay a Bayern Munich game, but not a Hoffenheim game."
As it stands, Bayer Leverkusen sit top of the Bundesliga.
Leverkusen head coach Sami Hyypia said: "I celebrated during the game because it looked like it was in, but of course now it's a bit uncomfortable.
"But I can't do anything about it - it's the referee who makes the decisions."