What should have been a joyous 6-0 away win for Bayern on Saturday was soured when the contest was halted during the second half after visiting fans held up banners insulting Hoffenheim owner Dietmar Hopp.
After the referee enforced the stoppage to facilitate the banners' removal following appeals from the Bayern players, the two teams saw out the rest of the match by passing the ball among themselves as a show of solidarity towards Hopp.
Bayern boss Hansi Flick and chairman Karl-Heinz Rummenigge apologised for what they described as "ugly" protests, while Hopp has told his critics he will not stop attending games.
In an open letter to supporters, Hainer joined the condemnation and will be involved in meetings to discuss the next steps that will be taken.
"All of us at FC Bayern are still stunned by yesterday's incidents in Hoffenheim," he wrote on Sunday.
"We are ashamed of the behaviour of a few so-called "fans" in the FC Bayern terrace and seating area during the game.
"Dietmar Hopp was insulted in the worst imaginable way by a few idiots with a banner. He was defamed, from a distance, anonymously, namelessly, and in a cowardly way. The events were an absolute low point.
"On behalf of the entire club, I would like to apologise once again to Dietmar Hopp for this!"
After reiterating the club's values of tolerance and respect, Hainer added: "We will not allow our club to be damaged by a tiny minority.
"[They are] people who are not concerned about football and FC Bayern, but about showing off on a stage that does not belong to them.
"It is high time to act decisively. Racism, exclusion, insults and discrimination of any kind and against anyone must stop now. This is also the opinion of the overwhelming majority of FC Bayern fans.
"In the next few days, the relevant bodies at FC Bayern Munich will meet and talk. We will examine all the options to prevent a repetition of events as undignified as those in Hoffenheim.
"We will also use all the means at our disposal to take decisive action against those who have discredited FC Bayern and the whole of German football, and trampled on our values."