The banner questioned how Qatari Al-Khelaifi could be a club owner, a UEFA Executive Committee member, the chairman of the European Club Association and a television rights holder as beIN chairman.
It called him "plutocratic" and used an expletive.
"FC Bayern would like to apologise when its opponents and their representatives in its stadium feel personally attacked in this manner and tone, and are offended as a result," Bayern said in a statement.
"The club would like to make it clear that these banners were not authorised by FC Bayern and do not reflect its stance. They are not in keeping with the good and long-standing relationship between the two clubs.
"The tone of these banners also goes against the style of FC Bayern and the respectful relationship the club has with its international partners."
Bayern beat PSG 1-0 thanks to Kim Min-jae's goal while the French side were reduced to 10 men when Ousmane Dembele was sent off just before the hour mark.
