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.
Despite the delay seemingly signifying a turning point in the tie, a Salzburg spookesman told Perform: "To judge about the things happened by the Basel fans in the stadium is the task of UEFA. For Red Bull Salzburg this case is closed.
"We are - at the moment - sad that we've lost the game against the Swiss champions.
"(But) also we will be happy to (have) played such a strong season in the Europa League."
