Hundreds of Dortmund fans were involved in the clashes in the stands of Toumba stadium in Thessaloniki during their 1-1 draw as well as after the end of the game.
The match was briefly interrupted after the break when flares once more were lit and some of them thrown towards the stadium's medical staff.
"Our fans started it. This cannot be tolerated," Watzke told reporters. "We had made things clear to the groups in question before the game. Now there will be a sensitive financial sanction against us. If the game is affect then a limit has been reached. This is no longer acceptable."
Dozens of riot police in full gear and wielding batons entered the tribune where some of the 1,400 visiting Dortmund fans were seated, detaining some supporters while also trying to break up the larger groups which had started the trouble.
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"We cannot talk our way out of this one," Watzke said. "It is a shame because the game was affected and for several minutes we were not watching what was happening on the pitch."
(Reporting by Karolos Grohmann; Editing by Amlan Chakraborty)
