The Kazakhstan club caused a stir when they slaughtered a sheep at the Astana Arena on the eve of their Champions League playoff round first-leg tie against Celtic last Tuesday.
Animal rights group PETA expressed outrage in a strongly worded letter to UEFA president Michel Platini, urging the organisation to punish Shakhter.
There were growing concerns that Shakhter would repeat the ritual at Celtic Park ahead of Wednesday night's return tie, which sees the visitors defend a 2-0 advantage.
UEFA competitions director Giorgio Marchetti has informed Shakhter executive director Yerden Khalilin disciplinary proceedings will follow should the club indulge in the ritual again.
Marchetti said: "We were informed that an animal slaughter took place at some point prior to the UEFA Champions League fixture involving FC Shakhter Karagandy and Celtic FC at the Astana Arena on Tuesday 20 August 2013.
"Although certain practices may be culturally rooted, they have no place in or around a sporting arena or event.
"In this context, I would like to make you aware that animal slaughter on a football pitch or in a stadium before, during or after a UEFA competition match - or with reference to a UEFA competition - is totally improper, and will not be tolerated.
"In case of re-occurrence, it will inevitably lead to a full investigation by our disciplinary bodies."