Legia midfielder Ondrej Duda was hit by a stone thrown from the crowd when his side had just taken a 2-1 lead.
Play was immediately suspended as Duda was stretchered off to have his head bandaged – the player was ready to return soon after but the restart never came.
Both teams have been charged over fans throwing objects. Kukesi also face charges of crowd disturbances, unfurling an illicit banner and match abandonment.
The case will be dealt with by the UEFA Control, Ethics and Disciplinary Body at its next meeting on August 3.
The return leg is scheduled for next Thursday.
It is the second consecutive season that Legia’s European participation has been marked by controversy.
They were thrown out of last season’s Champions League for fielding an ineligible player during a 6-1 aggregate win over Scottish champions Celtic.