Dortmund were confident they had scored against champions Bayern when Mats Hummels headed onto goal in the 64th minute and defender Dante cleared the ball near the line with the score at 0-0.
Television replays showed both Dante's leg and the ball, even further behind in goal, were clearly over the line.
Instead it was Bayern who struck twice in extra-time to lift the trophy and complete the domestic double.
The incident was the second major argument in favour of goalline technology this season with Bayer Leverkusen's Stefan Kiessling being awarded a goal against Hoffenheim earlier in the season despite the ball landing in goal through a hole in the sidenetting.
"If Dortmund CEO Hans Joachim Watzke or a representative of other clubs resuggests goalline technology, it would be something that I would support," German Football League (DFL) chief Reinhard Rauball, who is also the president of Borussia Dortmund, told Sueddeutsche newspaper on Monday.
Yet it was only as recently as March 24 that the 36 clubs from the first and second division rejected the introduction of the technology with half of the top-flight clubs voting in favour and only three of 18 second division teams backing the idea.
A two-thirds majority was necessary with many clubs against it because of the technology's cost. Rauball himself had said in March the issue was "now off the table".
Dortmund were left fuming after the Cup final with coach Juergen Klopp saying had the goal counted it would have changed the game but did not call for goalline technology.
"The ball was so far inside the goal that you do not need goalline technology," Klopp told reporters. "All my substitutes saw it and they were standing behind the goal."
DFL managing director Andreas Rettig on Monday also hinted the issue could now come back as long as it was the clubs who demanded a new vote on the technology.
"If it is the wish of the clubs then there is nothing in the way of a new vote. The DFL is well prepared," Rettig told reporters.
The English top-flight became the first domestic league to use technology in August and the system worked well throughout the entire season.
Dubbed Goal Decision System (GDS) and developed by the Hawk-Eye company, the system gives referees a ruling within a second, their watch buzzing to tell them when the ball has gone in.
Goalline technology will also be in use at the World Cup in Brazil in June and July.
- Sports & Recreation
- Borussia Dortmund