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.
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.
