The Dons lodged an official complaint with Europe’s governing body following the opening leg of their first qualifying round tie at the National Stadium.
In a statement, UEFA said: “Disciplinary proceedings have been opened against Shkendija for use of a laser pointer - Article 16 (2) of the UEFA Disciplinary Regulations.
“This case will be dealt with by the UEFA Control Ethics and Disciplinary body on its next meeting on 23 July.”
The disciplinary panel’s decision will be announced in the days following the meeting.
Aberdeen will welcome Shkendija to the Granite City on Thursday after last week’s 1-1 draw.
Niall McGinn put the Scots in front with 12 minutes remaining, but they could not hold on for the win as Hristijan Kirovski’s header squared the tie ahead of this week’s return.
But the Reds were unhappy with the action of the home fans in Skopje after Ward, signed on loan from Liverpool, had the laser shone in his eyes during the match and contacted UEFA’s delegate after the final whistle to make their complaint.