The former West Germany was disappointed by the outcome of Monday's meeting in Frankfurt, while Mainz boss Thomas Tuchel says he is baffled by the decision.
Bayern Munich chairman Karl-Heinz Rummenigge has expressed his "regret" at seeing clubs from Germany's top two leagues vote against the introduction of goal-line technology.
In order to be passed, the proposal required the support of at least 12 sides from both the Bundesliga and 2.Bundesliga - a two-thirds majority in each championship.
However, of the 36 clubs present at Monday's meeting in Frankfurt, nine top-tier teams and 15 second division sides voted against allowing match officials to avail of technology in order to confirm whether a ball had cross the goal-line.
"Democratically, we have to accept it," Rummenigge told reporters afterwards. "But we regret the decision at Bayern."
Mainz boss Mainz boss Thomas Tuchel went further, stating that he was utterly bemused by the outcome of the vote.
"For me, it is incomprehensible that it has been rejected," he said. "I can't understand it."
Meanwhile, the chairman of the German Football Association's (DFB) referee commission, Herbert Fandel, hinted that he too was disappointed by the decision.
"We referees have always said that we would welcome the introduction of goal-line technology," he stated. "It supports the referees in the most important decision of football and also takes away a little of the criticism.
"The fact that the professional clubs have now spoken mostly on the other hand, we accept of course."
Goal-line technology is already being utilized in the Premier League and will be available to officials at this year's World Cup in Brazil.