The teams went into the last 16 encounter goalless from the first leg, but Salzburg were soon on the front foot at the Red Bull Arena as Jonatan Soriano fired them in front after Marek Suchy had been sent off for the visitors.
However, objects hurled from an area of the ground containing Basel fans prompted Salzburg players to leave the field during the first half and play was suspended for 13 minutes.
When the match did resume, Basel managed to turn the tie on its head with goals from Marco Streller and Gaston Sauro before the hosts had Alan sent off for a second bookable offence.
Salzburg confirmed to Perform earlier on Friday that they would not be pursuing punishment for their Swiss opponents, but UEFA have now opted to take action.
A statement read: "Disciplinary proceedings have been opened against FC Basel 1893 for setting-off and throwing of fireworks (art. 16 (2) DR) and improper conduct of the team (art. 15 (4) DR).
"The case will be dealt by the UEFA Control and Disciplinary Body at its next meeting on Wednesday 26 March."
Basel were drawn to face Sevilla in Friday's quarter-final draw in Nyon.
