The governing body listed “insufficient organisation”, “field invasions by supporters” and “stairways blocked” among its concerns that arose during the 2-2 draw.
The same action is being taken against the Polish Football Federation.
Incidents listed by Uefa concerning the PZPN include “kit infringement”, “setting off and throwing of fireworks”, “throwing of objects”, and “crowd disturbances”.
In addition to a young Scotland supporter entering the pitch during the second half to have a photo taken with Poland’s Robert Lewandowksi, whose 94th-minute equalising goal ended Scotland’s hopes of reaching next summer’s tournament, Poland’s fans could be seen setting off flares in the away end.
Police Scotland has confirmed that a total of 21 arrests were made throughout the course of the match.
Each were for “minor disorders”, with no major incidents reported, and those involved included fans for each team.
Uefa’s disciplinary proceedings are to be held on October 22