Basel were trailing 1-0 at the time when the two teams were led off in the 30th minute at the start of a 12-minute delay.
Referee Manuel Grafe took the players off when Salzburg's Kevin Kampl was targetted by a bottle while cigarette lighters were also thrown onto the pitch.
Basel's Marek Suchy had been red-carded in the ninth minute but Marco Streller (50 minutes) and Gaston Sauro (60) scored from second-half set pieces to cancel out Jonatan Soriano's 22nd-minute volley.
The draw for the quarter-finals takes place on Friday with the ties on April 3rd and 10th.
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